UMI in BCBIO
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Vincent Funari
Jun 9, 2017, 6:33:06 PM6/9/17
to biovalidation, Jeffrey Day, Vincent Funari
Good Evening Brad,
I see Nils, Tim and you were working a while back on implementing fbio scripts into bcbio for handling umi's used to remove any amplification bias, which is especially important in amplicon sequencing or deep sequencing.
Not clear on the instructions on how to use BCBIO for amplicon variant analysis with UMIs
In general i think its
1. Generate a FASTQ UMI
2. Get a BAM file with filtered reads
3. Annotate the BAM file with UMIs
4. Generate Consensus reads
The first step I can do with BCL->FASTQ or your tool. Or would this command do the same thing with your tool:
I see Nils, Tim and you were working a while back on implementing fbio scripts into bcbio for handling umi's used to remove any amplification bias, which is especially important in amplicon sequencing or deep sequencing.
Not clear on the instructions on how to use BCBIO for amplicon variant analysis with UMIs
In general i think its
1. Generate a FASTQ UMI
2. Get a BAM file with filtered reads
3. Annotate the BAM file with UMIs
4. Generate Consensus reads
The first step I can do with BCL->FASTQ or your tool. Or would this command do the same thing with your tool:
>bcbio_fastq_umi_prep.py autopair -c 8 r1.fastq r2.fastq > umi.out.fastq
Then I can run bcbio for the alignment,
but how do you annotate the bam file with UMI and
then how do you make consensus reads in side bcbio.
Sorry Its not clear from the online manual?
Thanks in advance
Brad Chapman
Jun 10, 2017, 5:36:16 AM6/10/17
to Vincent Funari, biovalidation, Jeffrey Day, Vincent Funari
Vincent;
Thanks for checking on the UMI support. That's all exactly right, first you
use `bcbio_fastq_umi_prep.py` to add UMIs directly to the input fastq files.
That script moves UMIs from a third file into the fastq name. Then you set
`umi_type: fastq_name` and bcbio handles annotating the aligned BAM with UMIs,
grouping reads by UMI and position, and calling consensus reads:
http://bcbio-nextgen.readthedocs.io/en/latest/contents/configuration.html#umis
Please let us know if you have any other questions,
Brad
> [ text/plain ]
> Good Evening Brad,
> I see Nils, Tim and you were working a while back on implementing fbio
> scripts into bcbio for handling umi's used to remove any amplification
> bias, which is especially important in amplicon sequencing or deep
> sequencing.
>
> Not clear on the instructions on how to use BCBIO for amplicon variant
> analysis with UMIs
>
> In general i think its
> 1. Generate a FASTQ UMI
> 2. Get a BAM file with filtered reads
> 3. Annotate the BAM file with UMIs
> 4. Generate Consensus reads
>
> The first step I can do with BCL->FASTQ or your tool. Or would this command
> do the same thing with your tool:
>
>>bcbio_fastq_umi_prep.py autopair -c 8 r1.fastq r2.fastq > umi.out.fastq
>
> Then I can run bcbio for the alignment,
> but how do you *annotate the bam* file with UMI and
> I see Nils, Tim and you were working a while back on implementing fbio
> scripts into bcbio for handling umi's used to remove any amplification
> bias, which is especially important in amplicon sequencing or deep
> sequencing.
>
> Not clear on the instructions on how to use BCBIO for amplicon variant
> analysis with UMIs
>
> In general i think its
> 1. Generate a FASTQ UMI
> 2. Get a BAM file with filtered reads
> 3. Annotate the BAM file with UMIs
> 4. Generate Consensus reads
>
> The first step I can do with BCL->FASTQ or your tool. Or would this command
> do the same thing with your tool:
>
>>bcbio_fastq_umi_prep.py autopair -c 8 r1.fastq r2.fastq > umi.out.fastq
>
> Then I can run bcbio for the alignment,
> then how do you make *consensus reads* in side bcbio.
>
> Sorry Its not clear from the online manual?
>
> Thanks in advance
>
>
>
>
>
> --
> Sorry Its not clear from the online manual?
>
> Thanks in advance
>
>
>
>
>
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Vincent Funari
Jun 14, 2017, 8:20:50 PM6/14/17
to biovalidation, funar...@gmail.com, jeffre...@gmail.com, vfu...@neogenomics.com
Thanks,
So it looks like this works with a single UMI. We have a UMI on read1 and another UMI on Read2 in our paired end amplicon data. I think right now there are 2 commercial vendors that support this design for variant calling Qiagen (QiaSeq) and Agilent (HaloplexHS). I can easily generate fastq files that contain the UMIs for each Read (e.g. UMIR1.fastq and UMIR2.fastq). Is there a way we can use these two reads in your system.
Luca Beltrame
Jun 15, 2017, 10:57:55 AM6/15/17
to bioval...@googlegroups.com
In data giovedì 15 giugno 2017 02:20:50 CEST, Vincent Funari ha scritto:
> Qiagen (QiaSeq) and Agilent (HaloplexHS). I can easily generate fastq files
> that contain the UMIs for each Read (e.g. UMIR1.fastq and UMIR2.fastq). Is
Would you mind sharing some pointers on how to do that? We're starting working
> Qiagen (QiaSeq) and Agilent (HaloplexHS). I can easily generate fastq files
> that contain the UMIs for each Read (e.g. UMIR1.fastq and UMIR2.fastq). Is
with QIAGEN kits, which implement thist ype of UMI as far as I understand, so
it would be helpful.
--
Luca Beltrame, Ph.D.
Translational Genomics Unit, Department of Oncology
IRCCS Istituto di Ricerche Farmacologiche "Mario Negri"
VINCENT FUNARI
Jun 15, 2017, 12:15:26 PM6/15/17
to luca.b...@marionegri.it, bioval...@googlegroups.com, jeffr...@neogenomics.com
Ciao luca,
Jeff can u please post our 4-5 lines of code to create the 2 umi fastq files from qiagen qiaseq. We use a couple of features of 2 adapter programs. It can probably be done more elegantly but it works fine if you build your shell script with these. Luca we also really like the qiaseq chemistry in the lab so any progress here would be great.
Thank you,
Sent from my iPhone
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Jeff can u please post our 4-5 lines of code to create the 2 umi fastq files from qiagen qiaseq. We use a couple of features of 2 adapter programs. It can probably be done more elegantly but it works fine if you build your shell script with these. Luca we also really like the qiaseq chemistry in the lab so any progress here would be great.
Thank you,
Sent from my iPhone
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VINCENT FUNARI
Jun 15, 2017, 8:17:00 PM6/15/17
to luca.b...@marionegri.it, bioval...@googlegroups.com
Luca
Please see below for how we clean and separate the UMI/Adapter from the paired-end QiaSeq panels. We will still have to deal with unpaired reads, but for now this should be a good start to figure out how to annotate/compress the UMIs in the BAM.
Read2.is pretty easy
To generate a clean fastq that does not contain adapter/UMI, we first remove the 23 bp of the 5' side of the read. This is the 12-mer UMI plus the 11 bp common ligation adapter ATTGGAGTCCT.
>java -jar trimmomatic-0.36.jar SE Qiaseq/Input _S1_R2_001.fastq.gz QiaSeq/out_cleaned_R2.fastq HEADCROP:23
Then in order to create a UMI.fastq for Read 2 we use the following command which just
>java -jar trimmomatic-0.36.jar SE QiaSeq/input _S1_R2_001.fastq.gz QiaSeq/output.UMI.fastq CROP:12
Read 1 is a little more complicated
To generate a clean fastq
Discard 11mer adapter (AGGACTCCAAT) and everything after that from the 3' side of the read. This is the reverse complement of the 11 bp common ligation adapter and the 12 bp UMI. Not all reads will have this full sequence, because the read fragments have random lengths (most are 40 to 400 bp) so the trim must be aggressive. i.e. if the read ends in AGG, go ahead and trim it, even if the AGG is sometimes endogenous.
>cutadapt -a AGGACTCCAAT –o QiaSeq/out_cleaned_S1_R1_001.fastq.gz QiaSeq/input_R1_001.fastq.gz
To Create UMI-Read1.fastq
#First generate an intermediate FASTQ file that has UMI plus some garbage on 3’ end. To do this, first CUT OFF ADAPTER AND 5'END OF READ SO THAT YOU only HAVE the UMI AT END PLUS ANY GARBAGE TO TRIM LATER
>cutadapt -g AGGACTCCAAT -o QiaSeq/Read1.UMI-R1-intermediate.fastq QiaSeq/input_R1_001.fastq.gz
#Then the next step is to create the final UMI fastq for R1: by using CROP on the intermediate.fastq file. The output is the UMI-R1.fastq.
>java -jar trimmomatic-0.36.jar SE QiaSeq/Read1.UMI-R1-final.fastq.gz QiaSeq/Read1.UMI-R1-intermediate.fastq CROP:12
Sent from my iPhone
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Brad Chapman
Jun 16, 2017, 8:37:47 AM6/16/17
to VINCENT FUNARI, luca.b...@marionegri.it, bioval...@googlegroups.com
Vincent, Luca and Jeffrey;
Thanks for this discussion and sharing the scripts you use. We finished adding
support for duplex tags in read 1 and read 2 in the latest development version
of bcbio. This works identically to having separate UMIs except that it trims
and extracts the tags from the reads:
http://bcbio-nextgen.readthedocs.io/en/latest/contents/configuration.html#umis
For variant calling this feeds into the same consensus read generation
process, using fgbio for duplex support. The main trickiness is naming schemes
for the UMIs/barcodes, which this resolves using the same sort of tags used in
single cell.
Vincent and Jeffrey -- hopefully this would help avoid some of the need to
manually pre-process and fit into your workflow. Hope this helps and thanks
again,
Brad
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Vincent Funari
Jun 16, 2017, 5:24:31 PM6/16/17
to biovalidation, funar...@gmail.com, luca.b...@marionegri.it
Thank you Brad
I noticed that the command at the bottom works for 5' only UMIs in both reads. In Qiaseq and others the UMIs are not always 5' for both reads. For read 1 it is actually random depending on the read length of the molecule, So its not always present and the only way to identify it is because it is 3'/downstream of an adapter sequence in the read. Also I am not clear what tag1/tag2 represent here since the UMIs are unique.
Maybe this can be simplified is there a way to enter your python script with 2 UMI FASTQs? Then go from there, that would make it kind of universal and we wouldnt have to worry about UMI designs?
> bcbio_fastq_umi_prep.py single --tag1 5 --tag2 5 <out basename> <read 1 fastq> <read 2 fastq>
Brad Chapman
Jun 17, 2017, 6:07:23 AM6/17/17
to Vincent Funari, biovalidation, funar...@gmail.com, luca.b...@marionegri.it
Vincent;
Thanks much for looking into the implementation. For custom filtering that
requires something more complex like finding adapters and trimming next to
those, I agree this will likely not be sufficient. What I'd recommend is doing
that trimming/preparation upstream and generating 3 files: Read 1, Read 2, and
the final UMI. Then you can use the `bcbio_fastq_umi_prep.py` script to put
the UMIs into the read name:
bcbio_fastq_umi_prep.py single <out basename> <read 1 fastq> <read 2 fastq> <umi fastq>
or have it add the UMIs to the BAMs directly in bcbio by specifying:
umi_type: /path/to/umi.fq
Either way bcbio will then do the UMI grouping and consensus calling.
You can prep the UMIs either as a duplex tag separated with a `-`:
UMI1-UMI2
or just as one big UMI concatenated together:
UMI1UMI2
Both should work and provide reasonable results and we're still benchmarking
how the methods compare.
Hope this helps,
Brad
> [ text/plain ]
>> <javascript:>> wrote:
>> >>
>> >> In data giovedì 15 giugno 2017 02:20:50 CEST, Vincent Funari ha
>> scritto:
>> >>
>> >>> Qiagen (QiaSeq) and Agilent (HaloplexHS). I can easily generate fastq
>> files
>> >>> that contain the UMIs for each Read (e.g. UMIR1.fastq and
>> UMIR2.fastq). Is
>> >>
>> >> Would you mind sharing some pointers on how to do that? We're starting
>> working
>> >> with QIAGEN kits, which implement thist ype of UMI as far as I
>> understand, so
>> >> it would be helpful.
>> >>
>> >> --
>> >> Luca Beltrame, Ph.D.
>> >> Translational Genomics Unit, Department of Oncology
>> >> IRCCS Istituto di Ricerche Farmacologiche "Mario Negri"
>> >>
>> >> --
>> >> You received this message because you are subscribed to a topic in the
>> Google Groups "biovalidation" group.
>> >> To unsubscribe from this topic, visit
>> https://groups.google.com/d/topic/biovalidation/A88NehFSOrM/unsubscribe.
>> >> To unsubscribe from this group and all its topics, send an email to
>> biovalidatio...@googlegroups.com <javascript:>.
>> >>
>> >> In data giovedì 15 giugno 2017 02:20:50 CEST, Vincent Funari ha
>> scritto:
>> >>
>> >>> Qiagen (QiaSeq) and Agilent (HaloplexHS). I can easily generate fastq
>> files
>> >>> that contain the UMIs for each Read (e.g. UMIR1.fastq and
>> UMIR2.fastq). Is
>> >>
>> >> Would you mind sharing some pointers on how to do that? We're starting
>> working
>> >> with QIAGEN kits, which implement thist ype of UMI as far as I
>> understand, so
>> >> it would be helpful.
>> >>
>> >> --
>> >> Luca Beltrame, Ph.D.
>> >> Translational Genomics Unit, Department of Oncology
>> >> IRCCS Istituto di Ricerche Farmacologiche "Mario Negri"
>> >>
>> >> --
>> >> You received this message because you are subscribed to a topic in the
>> Google Groups "biovalidation" group.
>> >> To unsubscribe from this topic, visit
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>> <javascript:>.
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>> >
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Vincent Funari
Jun 26, 2017, 10:26:53 AM6/26/17
to biovalidation, funar...@gmail.com, luca.b...@marionegri.it, Jeffrey Day
Good Morning Brad
We were able to successfully run the UMI prep tools which did insert the UMIs into the FASTQ. We also set up the YAML with the UMI_type with the path to the umi fastq file. We set up the tumor only yaml file for BWA alignment and then Vardict with mark duplicates set to true. The alignment worked but there is no evidence of any other UMI tool running. The VCF and BAM file didnt look any different than if we had not used the UMIs. So we checked the log and command log files to confirm the UMI toolls wer running and there wasnt anyting different about them. So Im not sure they are being called from the yaml, We updated to the latest BCBIO development.
What are we missing?
How can we verify its working?
thanks
We were able to successfully run the UMI prep tools which did insert the UMIs into the FASTQ. We also set up the YAML with the UMI_type with the path to the umi fastq file. We set up the tumor only yaml file for BWA alignment and then Vardict with mark duplicates set to true. The alignment worked but there is no evidence of any other UMI tool running. The VCF and BAM file didnt look any different than if we had not used the UMIs. So we checked the log and command log files to confirm the UMI toolls wer running and there wasnt anyting different about them. So Im not sure they are being called from the yaml, We updated to the latest BCBIO development.
What are we missing?
How can we verify its working?
thanks
Brad Chapman
Jun 26, 2017, 2:45:50 PM6/26/17
to Vincent Funari, biovalidation, funar...@gmail.com, luca.b...@marionegri.it, Jeffrey Day
Vincent;
Thanks for following up. It sounds like you did things right but I'm not sure
without seeing the YAML file why it would not do the UMI consensus processing
after alignment. Did you have `umi_type: fastq_name` in your YAML configuration?
http://bcbio-nextgen.readthedocs.io/en/latest/contents/configuration.html#umis
If that doesn't explain it, could you share your YAML file and I'd be happy to
try and offer more specific ideas. Thanks much for the help debugging,
Brad
> [ text/plain ]
Vincent Funari
Jun 26, 2017, 3:29:02 PM6/26/17
to biovalidation, funar...@gmail.com, luca.b...@marionegri.it, jeffre...@gmail.com
details:
- algorithm:
aligner: bwa
clinical_reporting: true
coverage_depth_min: 100
ensemble:
numpass: 1
indelcaller: false
mark_duplicates: true
min_allele_fraction: 0.01
min_read_length: 50
remove_lcr: true
umi_type: /isilon/scratch/QiaSeq/QiaSeq-042117-37323287/UMI1UMI2.fastq
variant_regions: /isilon/scratch/DHS-3501Z.roi.bed
variantcaller:
- vardict
analysis: variant2
description: NTP17.annotated_R1
files:
- /isilon/scratch/NS-Test4/NTP17.annotated_R1.fq.gz
- /isilon/scratch/NS-Test4/NTP17.annotated_R2.fq.gz
genome_build: hg19
metadata:
batch: Batch1
phenotype: tumor
fc_date: '2017-06-22'
fc_name: NS-Test4
upload:
dir: ../final
Brad Chapman
Jun 27, 2017, 6:25:36 AM6/27/17
to Vincent Funari, biovalidation, funar...@gmail.com, luca.b...@marionegri.it, jeffre...@gmail.com
Vincent;
Thanks for posting this. As mentioned below, I'd recommend using:
umi_type: fastq_name
if you've run the bcbio pre-processing since the UMIs get embedded in the read
names by that script and we can then stream them following alignment.
Beyond that I'm still not sure why you wouldn't see any UMI work, even with
the current configuration. fgbio should be run whenever you have
mark_duplicates and umi_type specified. To be clear, there are no fgbio
commands in your `log/bcbio-nextgen-commands.log`?
Sorry to not be sure what to suggest and thanks for the help debugging,
Vincent Funari
Jun 27, 2017, 4:19:17 PM6/27/17
to biovalidation, funar...@gmail.com, luca.b...@marionegri.it, jeffre...@gmail.com, Vincent Funari
Hi Brad,
Thank you for your help! As you can see from the yaml below we did include that umi_type line and mark_duplicates: true.
Also, Ive attached a picture of the BAM showing the reads with UMI in the read name were aligned just fine.
I've also added the command log which shows there is no fgbio being called in command line (thanks for that hint!).
We are using the latest development version. Might be good for us to try an example dataset for variant analysis to make sure our system is working, I did confirm fgbio is installed runs fine from commandline, but somehow as you can see from the commands log its not being called by bcbio.
Thank you!
Brad Chapman
Jun 28, 2017, 8:32:04 AM6/28/17
to Vincent Funari, biovalidation, funar...@gmail.com, luca.b...@marionegri.it, jeffre...@gmail.com, Vincent Funari
Vincent;
Thanks for following up. Sorry for any confusion, what I meant was to change
the YAML to:
umi_type: fastq_name
rather than the path to the UMI file. Since the bcbio script put the UMI in
the name you no longer need the external UMI file. What I think happens is
that the path to the UMI file is incorrect so bcbio doesn't find it and just
skips doing UMI analysis altogether. Hopefully that change gets it working for
you,
Brad
> [ text/plain ]
>
>
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>
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> [2017-06-27T15:27Z] /usr/local/share/bcbio/galaxy/../anaconda/bin/bgzip --threads 8 -c /isilon/scratch/NS-JeffTest4/NTP17-002714.annotated_R2.fq > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpFrc2YD/NTP17-002714.annotated_R2.fq.gz
> [2017-06-27T15:27Z] /usr/local/share/bcbio/galaxy/../anaconda/bin/bgzip --threads 8 -c /isilon/scratch/NS-JeffTest4/NTP17-002714.annotated_R1.fq > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpJk9RIV/NTP17-002714.annotated_R1.fq.gz
> [2017-06-27T15:28Z] /usr/local/share/bcbio/galaxy/../anaconda/bin/grabix index /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp79h3ky/NTP17-002714.annotated_R1.fq.gz
> [2017-06-27T15:28Z] /usr/local/share/bcbio/galaxy/../anaconda/bin/grabix index /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp1CRxGq/NTP17-002714.annotated_R2.fq.gz
> [2017-06-27T15:28Z] unset JAVA_HOME && /usr/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NTP17-002714_annotated_R1\tPL:illumina\tPU:1_2017-06-27_NS-JeffTest4\tSM:NTP17-002714_annotated_R1' -v 1 /usr/local/share/bcbio/genomes/Hsapiens/hg19/bwa/hg19.fa /isilon/scratch/NS-JeffTest4/work/align_prep/NTP17-002714_annotated_R1_NTP17-002714.annotated_R1.fq.gz /isilon/scratch/NS-JeffTest4/work/align_prep/NTP17-002714_annotated_R1_NTP17-002714.annotated_R2.fq.gz | bamsormadup inputformat=sam threads=16 tmpfile=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpprTcgt/NTP17-002714_annotated_R1-sort-sorttmp-markdup SO=coordinate indexfilename=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpprTcgt/NTP17-002714_annotated_R1-sort.bam.bai > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpprTcgt/NTP17-002714_annotated_R1-sort.bam
> [2017-06-27T15:29Z] /usr/local/share/bcbio/galaxy/../anaconda/bin/sambamba index -t 16 /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpH9H4E9/NTP17-002714_annotated_R1-sort.bam.bai
> [2017-06-27T15:29Z] cat /isilon/scratch/DHS-3501Z.roi.bed | grep -v ^track | grep -v ^browser | grep -v ^# | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.bedutils.remove_bad(x)' | sort -V -k1,1 -k2,2n > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpgvOLrE/DHS-3501Z.roi.bed
> [2017-06-27T15:29Z] cat /isilon/scratch/NS-JeffTest4/work/bedprep/DHS-3501Z.roi.bed | /usr/local/share/bcbio/galaxy/../anaconda/bin/bgzip --threads 16 -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmppzMmGi/DHS-3501Z.roi.bed.gz
> [2017-06-27T15:29Z] /usr/local/share/bcbio/galaxy/../anaconda/bin/tabix -f -p bed /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpQDBW3H/DHS-3501Z.roi.bed.gz
> [2017-06-27T15:29Z] /usr/local/share/bcbio/galaxy/../anaconda/bin/bedtools merge -i /isilon/scratch/NS-JeffTest4/work/bedprep/DHS-3501Z.roi.bed > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpZZzkcJ/DHS-3501Z.roi-merged.bed
> [2017-06-27T15:29Z] cat /isilon/scratch/NS-JeffTest4/work/bedprep/DHS-3501Z.roi-merged.bed | /usr/local/share/bcbio/galaxy/../anaconda/bin/bgzip --threads 16 -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpUNO6bt/DHS-3501Z.roi-merged.bed.gz
> [2017-06-27T15:29Z] /usr/local/share/bcbio/galaxy/../anaconda/bin/tabix -f -p bed /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp4vle_z/DHS-3501Z.roi-merged.bed.gz
> [2017-06-27T15:29Z] /usr/local/share/bcbio/galaxy/../anaconda/bin/sambamba depth region -t 16 /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -L /isilon/scratch/NS-JeffTest4/work/bedprep/DHS-3501Z.roi-merged.bed -F "not unmapped and not mate_is_unmapped and not secondary_alignment and not failed_quality_control and not duplicate" -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpglbMeK/variant_regions_regions_depth.bed
> [2017-06-27T15:30Z] goleft depth --q 1 --mincov 100 --processes 16 --ordered --reference /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort-bamref.fa --prefix /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpN7a4A8/NTP17-002714_annotated_R1-coverage /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam
> [2017-06-27T15:30Z] /usr/local/share/bcbio/galaxy/../anaconda/bin/sambamba view -c -t 1 /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -F "not unmapped and not mate_is_unmapped and not secondary_alignment and not failed_quality_control and not duplicate" > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp2Oi3QN/num_not_unmapped_and_not_mate_is_unmapped_and_not_secondary_alignment_and_not_failed_quality_control_and_not_duplicate
> [2017-06-27T15:30Z] /usr/local/share/bcbio/galaxy/../anaconda/bin/sambamba view -c -t 1 /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -L /isilon/scratch/NS-JeffTest4/work/bedprep/DHS-3501Z.roi-merged.bed -F "not unmapped and not mate_is_unmapped and not secondary_alignment and not failed_quality_control and not duplicate" > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpFmPAGa/num_not_unmapped_and_not_mate_is_unmapped_and_not_secondary_alignment_and_not_failed_quality_control_and_not_duplicate_on_variant_regions
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpGapbkd' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr13/Batch1-chr13_48881410_115169878-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpGapbkd/Batch1-chr13_48881410_115169878-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpRqxYpQ' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr8/Batch1-chr8_38272071_117859935-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpRqxYpQ/Batch1-chr8_38272071_117859935-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpomMazY' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr5/Batch1-chr5_56116567_112043584-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpomMazY/Batch1-chr5_56116567_112043584-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpjjbaVa' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr2/Batch1-chr2_46574006_136873514-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpjjbaVa/Batch1-chr2_46574006_136873514-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpDPJLuA' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr6/Batch1-chr6_33286514_106534475-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpDPJLuA/Batch1-chr6_33286514_106534475-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp9BNZMM' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr4/Batch1-chr4_0_55124989-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp9BNZMM/Batch1-chr4_0_55124989-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpPa7eoE' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr9/Batch1-chr9_21968718_80336434-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpPa7eoE/Batch1-chr9_21968718_80336434-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpL62hJ5' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr1/Batch1-chr1_65301073_115251280-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpL62hJ5/Batch1-chr1_65301073_115251280-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpjjXM3f' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr18/Batch1-chr18_0_42281802-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpjjXM3f/Batch1-chr18_0_42281802-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpZjqi08' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr4/Batch1-chr4_153245330_191154276-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpZjqi08/Batch1-chr4_153245330_191154276-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpIzqS7n' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr21/Batch1-chr21_0_36164912-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpIzqS7n/Batch1-chr21_0_36164912-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpHkInd4' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr3/Batch1-chr3_128200656_178916970-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpHkInd4/Batch1-chr3_128200656_178916970-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpmUtZ1w' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr2/Batch1-chr2_198257690_243199373-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpmUtZ1w/Batch1-chr2_198257690_243199373-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpXGkdn0' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr14/Batch1-chr14_35871594_81422199-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpXGkdn0/Batch1-chr14_35871594_81422199-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpBAAKSI' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr1/Batch1-chr1_150550714_193091466-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpBAAKSI/Batch1-chr1_150550714_193091466-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpt82IzE' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr2/Batch1-chr2_136875610_178096747-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpt82IzE/Batch1-chr2_136875610_178096747-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpZEp6Cz' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr12/Batch1-chr12_69202982_112856934-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpZEp6Cz/Batch1-chr12_69202982_112856934-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp097vyi' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr8/Batch1-chr8_0_38271812-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp097vyi/Batch1-chr8_0_38271812-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpU6280b' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr7/Batch1-chr7_0_41730145-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpU6280b/Batch1-chr7_0_41730145-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpopRBEU' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr7/Batch1-chr7_41739579_81332078-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpopRBEU/Batch1-chr7_41739579_81332078-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp9iQY5i' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr10/Batch1-chr10_0_43572784-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp9iQY5i/Batch1-chr10_0_43572784-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpUD6vEA' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chrX/Batch1-chrX_63409753_100604949-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpUD6vEA/Batch1-chrX_63409753_100604949-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp2CrKZ0' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr10/Batch1-chr10_43595901_89624310-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp2CrKZ0/Batch1-chr10_43595901_89624310-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpg2pACa' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr4/Batch1-chr4_106162490_153244306-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpg2pACa/Batch1-chr4_106162490_153244306-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpwnXxzb/Batch1-chr18_0_42281802-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpEzn2vj/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr18/Batch1-chr18_0_42281802-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpEzn2vj/Batch1-chr18_0_42281802.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpZNL3Gr/Batch1-chr21_0_36164912-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpcJ6AOm/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr21/Batch1-chr21_0_36164912-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpcJ6AOm/Batch1-chr21_0_36164912.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp2i6wg8/Batch1-chr8_0_38271812-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpk4CJPt/Batch1-chr18_0_42281802.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpEtYAm4/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr8/Batch1-chr8_0_38271812-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpEtYAm4/Batch1-chr8_0_38271812.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp9oXZuB/Batch1-chr21_0_36164912.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpLQdOR2/Batch1-chr8_0_38271812.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpy3n5m6/Batch1-chr12_69202982_112856934-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpIozsk6/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr12/Batch1-chr12_69202982_112856934-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpIozsk6/Batch1-chr12_69202982_112856934.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpLftTbt/Batch1-chr12_69202982_112856934.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpuckV19/Batch1-chr4_153245330_191154276-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpXPnrfs/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr4/Batch1-chr4_153245330_191154276-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpXPnrfs/Batch1-chr4_153245330_191154276.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpiS68Qu/Batch1-chr14_35871594_81422199-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpe88l4g/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr14/Batch1-chr14_35871594_81422199-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpe88l4g/Batch1-chr14_35871594_81422199.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp_0S9St/Batch1-chr10_0_43572784-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpSm9D8Y/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr10/Batch1-chr10_0_43572784-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpSm9D8Y/Batch1-chr10_0_43572784.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpB559Ul/Batch1-chr4_153245330_191154276.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpJG6Kya/Batch1-chr14_35871594_81422199.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp3zBOjG/Batch1-chr10_0_43572784.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpYYfUmr/Batch1-chr6_33286514_106534475-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp8Sd6tU/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr6/Batch1-chr6_33286514_106534475-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp8Sd6tU/Batch1-chr6_33286514_106534475.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp8ysosT/Batch1-chr4_106162490_153244306-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpfHXHmN/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr4/Batch1-chr4_106162490_153244306-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpfHXHmN/Batch1-chr4_106162490_153244306.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpsobdPW/Batch1-chr6_33286514_106534475.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpcOCYNk' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr14/Batch1-chr14_0_35871271-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpcOCYNk/Batch1-chr14_0_35871271-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpeywQT8' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr5/Batch1-chr5_0_35857166-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpeywQT8/Batch1-chr5_0_35857166-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpNRgojz/Batch1-chr4_106162490_153244306.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpVwGM4t' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr9/Batch1-chr9_97869342_133589847-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpVwGM4t/Batch1-chr9_97869342_133589847-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpN0d96U' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr1/Batch1-chr1_115252184_150549972-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpN0d96U/Batch1-chr1_115252184_150549972-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpgEE72P' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr15/Batch1-chr15_33022885_66679770-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpgEE72P/Batch1-chr15_33022885_66679770-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmplko5w0' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr1/Batch1-chr1_193094236_226252185-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmplko5w0/Batch1-chr1_193094236_226252185-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpqKhNzP' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr15/Batch1-chr15_0_33010367-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpqKhNzP/Batch1-chr15_0_33010367-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpWImmkP/Batch1-chr14_0_35871271-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpDHO0Yt' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr11/Batch1-chr11_32410598_64572675-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpDHO0Yt/Batch1-chr11_32410598_64572675-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpMJNSLy/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr14/Batch1-chr14_0_35871271-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpMJNSLy/Batch1-chr14_0_35871271.vcf.gz -O z
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpYuIBsD' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chrX/Batch1-chrX_123159684_155270560-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpYuIBsD/Batch1-chrX_123159684_155270560-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp4jPcJw/Batch1-chr14_0_35871271.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpFC5AvZ/Batch1-chr15_0_33010367-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpNvJQn0/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr15/Batch1-chr15_0_33010367-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpNvJQn0/Batch1-chr15_0_33010367.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpFiA4Au/Batch1-chr15_0_33010367.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp0DFhH0' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr6/Batch1-chr6_106536070_138192664-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp0DFhH0/Batch1-chr6_106536070_138192664-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmplfDhee/Batch1-chr5_0_35857166-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp9Z1aSM/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr5/Batch1-chr5_0_35857166-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp9Z1aSM/Batch1-chr5_0_35857166.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpMxf_DN/Batch1-chr11_32410598_64572675-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpbPsyiw/Batch1-chr5_0_35857166.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpnkpEXC/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr11/Batch1-chr11_32410598_64572675-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpnkpEXC/Batch1-chr11_32410598_64572675.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmppLVu3E/Batch1-chr1_193094236_226252185-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpY4OD_v/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr1/Batch1-chr1_193094236_226252185-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpY4OD_v/Batch1-chr1_193094236_226252185.vcf.gz -O z
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpcpS1dO' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr3/Batch1-chr3_0_30648474-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpcpS1dO/Batch1-chr3_0_30648474-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpc9JtBu/Batch1-chr15_33022885_66679770-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpnsz7OO/Batch1-chr11_32410598_64572675.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpGEsHMA/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr15/Batch1-chr15_33022885_66679770-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpGEsHMA/Batch1-chr15_33022885_66679770.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpRhrplh/Batch1-chr1_193094236_226252185.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpqbHwB7/Batch1-chr15_33022885_66679770.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpqEXOlh/Batch1-chr9_21968718_80336434-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpO4c4YQ/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr9/Batch1-chr9_21968718_80336434-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpO4c4YQ/Batch1-chr9_21968718_80336434.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpAGyyNz/Batch1-chr13_48881410_115169878-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpvwZYaN/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr13/Batch1-chr13_48881410_115169878-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpvwZYaN/Batch1-chr13_48881410_115169878.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpfeERRS/Batch1-chr13_48881410_115169878.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpFAVid0/Batch1-chr9_21968718_80336434.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpbveJb0' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr2/Batch1-chr2_16085609_46525081-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpbveJb0/Batch1-chr2_16085609_46525081-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpzW6MvU' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr20/Batch1-chr20_0_30253894-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpzW6MvU/Batch1-chr20_0_30253894-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpl_qyob/Batch1-chr10_43595901_89624310-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpheJt4m/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr10/Batch1-chr10_43595901_89624310-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpheJt4m/Batch1-chr10_43595901_89624310.vcf.gz -O z
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpc3ajau' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr4/Batch1-chr4_55127256_84384060-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpc3ajau/Batch1-chr4_55127256_84384060-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmprIdnfd/Batch1-chr5_56116567_112043584-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpRYoKpc/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr5/Batch1-chr5_56116567_112043584-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpRYoKpc/Batch1-chr5_56116567_112043584.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpc6eN0J/Batch1-chr10_43595901_89624310.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpmIDgCh' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr13/Batch1-chr13_0_28578316-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpmIDgCh/Batch1-chr13_0_28578316-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpDvF3Bp/Batch1-chr2_198257690_243199373-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpODpqeg/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr2/Batch1-chr2_198257690_243199373-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpODpqeg/Batch1-chr2_198257690_243199373.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpMktl8J/Batch1-chr5_56116567_112043584.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmps4p3EY/Batch1-chr2_136875610_178096747-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpb0nxJ3' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr8/Batch1-chr8_117861179_146364022-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpb0nxJ3/Batch1-chr8_117861179_146364022-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpCS9MB6/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr2/Batch1-chr2_136875610_178096747-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpCS9MB6/Batch1-chr2_136875610_178096747.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp9elvWM/Batch1-chr7_41739579_81332078-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpOHsENQ/Batch1-chr1_65301073_115251280-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpNbsGqi/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr7/Batch1-chr7_41739579_81332078-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpNbsGqi/Batch1-chr7_41739579_81332078.vcf.gz -O z
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpwkb_wA/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr1/Batch1-chr1_65301073_115251280-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpwkb_wA/Batch1-chr1_65301073_115251280.vcf.gz -O z
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpPw2fh5' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr1/Batch1-chr1_36932825_65300345-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpPw2fh5/Batch1-chr1_36932825_65300345-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpa6ZnwD/Batch1-chr2_198257690_243199373.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpLMSQll/Batch1-chr7_0_41730145-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpMKXdgx/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr7/Batch1-chr7_0_41730145-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpMKXdgx/Batch1-chr7_0_41730145.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpxJyyh7/Batch1-chr1_65301073_115251280.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpRjV0Fc/Batch1-chr1_150550714_193091466-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpv96HFE/Batch1-chr2_136875610_178096747.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpfFehAA/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr1/Batch1-chr1_150550714_193091466-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpfFehAA/Batch1-chr1_150550714_193091466.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp0mS9AK/Batch1-chr7_41739579_81332078.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpapXOcG/Batch1-chr7_0_41730145.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpw6pSg0/Batch1-chr20_0_30253894-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpEHb_cF/Batch1-chr4_0_55124989-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpjDN5VH/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr20/Batch1-chr20_0_30253894-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpjDN5VH/Batch1-chr20_0_30253894.vcf.gz -O z
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpeTJwDY/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr4/Batch1-chr4_0_55124989-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpeTJwDY/Batch1-chr4_0_55124989.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmptXWjQz/Batch1-chr1_150550714_193091466.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpWmaqzZ/Batch1-chr3_128200656_178916970-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpVLMgpH/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr3/Batch1-chr3_128200656_178916970-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpVLMgpH/Batch1-chr3_128200656_178916970.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpYmTsiF/Batch1-chr13_0_28578316-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpNipz_3/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr13/Batch1-chr13_0_28578316-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpNipz_3/Batch1-chr13_0_28578316.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpBcFast/Batch1-chr20_0_30253894.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpcGscdH' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr7/Batch1-chr7_101460614_128829328-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpcGscdH/Batch1-chr7_101460614_128829328-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpACJwh4/Batch1-chr4_0_55124989.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp3Y5DLm/Batch1-chr3_128200656_178916970.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpk1moEP/Batch1-chr13_0_28578316.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpjaO3Qk' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr16/Batch1-chr16_23619179_50784118-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpjaO3Qk/Batch1-chr16_23619179_50784118-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp5ulRDq' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr6/Batch1-chr6_0_26032293-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp5ulRDq/Batch1-chr6_0_26032293-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpdc5821' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr12/Batch1-chr12_0_25362850-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpdc5821/Batch1-chr12_0_25362850-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpV6Dtf3' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chrX/Batch1-chrX_15809051_39911658-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpV6Dtf3/Batch1-chrX_15809051_39911658-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpQkQGrl/Batch1-chr2_46574006_136873514-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpuZWBQh/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr2/Batch1-chr2_46574006_136873514-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpuZWBQh/Batch1-chr2_46574006_136873514.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpUZuAGn/Batch1-chr8_38272071_117859935-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmppX0QI6' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chrX/Batch1-chrX_39913133_63406059-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmppX0QI6/Batch1-chrX_39913133_63406059-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpbE4URy/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr8/Batch1-chr8_38272071_117859935-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpbE4URy/Batch1-chr8_38272071_117859935.vcf.gz -O z
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpwNeMIt' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr16/Batch1-chr16_0_23614995-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpwNeMIt/Batch1-chr16_0_23614995-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpgmWVo3/Batch1-chr2_46574006_136873514.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmplwwHj0/Batch1-chr8_38272071_117859935.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp7QNZvf' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr10/Batch1-chr10_112328690_135534747-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp7QNZvf/Batch1-chr10_112328690_135534747-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpSIoKe8' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr12/Batch1-chr12_46124994_69202276-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpSIoKe8/Batch1-chr12_46124994_69202276-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpqvKZsU' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr3/Batch1-chr3_105389071_128200166-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpqvKZsU/Batch1-chr3_105389071_128200166-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpJWFRvW' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr10/Batch1-chr10_89653776_112327594-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpJWFRvW/Batch1-chr10_89653776_112327594-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpiHaYRu' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr3/Batch1-chr3_47059122_69788857-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpiHaYRu/Batch1-chr3_47059122_69788857-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpQIZpgk/Batch1-chr8_117861179_146364022-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpyBQgly/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr8/Batch1-chr8_117861179_146364022-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpyBQgly/Batch1-chr8_117861179_146364022.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp3ljVtA/Batch1-chr9_97869342_133589847-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpWKMsKz/Batch1-chr8_117861179_146364022.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpj3WmjY/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr9/Batch1-chr9_97869342_133589847-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpj3WmjY/Batch1-chr9_97869342_133589847.vcf.gz -O z
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpKk3KXO' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chrX/Batch1-chrX_100608176_123156526-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpKk3KXO/Batch1-chrX_100608176_123156526-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp1VpxeO/Batch1-chrX_63409753_100604949-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp_xz4rC/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chrX/Batch1-chrX_63409753_100604949-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp_xz4rC/Batch1-chrX_63409753_100604949.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpMJYhJj/Batch1-chr9_97869342_133589847.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpd89t4y' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr11/Batch1-chr11_0_22647361-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpd89t4y/Batch1-chr11_0_22647361-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpUBrCJ7/Batch1-chr16_23619179_50784118-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp1yiSJd/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr16/Batch1-chr16_23619179_50784118-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp1yiSJd/Batch1-chr16_23619179_50784118.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpsNzh7w/Batch1-chrX_63409753_100604949.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpLo6AwE/Batch1-chr16_23619179_50784118.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpEyRTv7/Batch1-chr12_0_25362850-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpoCthwp/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr12/Batch1-chr12_0_25362850-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpoCthwp/Batch1-chr12_0_25362850.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpV7N1wn/Batch1-chr1_115252184_150549972-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpTrVpzM/Batch1-chrX_15809051_39911658-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpBIBgNk/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr1/Batch1-chr1_115252184_150549972-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpBIBgNk/Batch1-chr1_115252184_150549972.vcf.gz -O z
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpKRm4Gp/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chrX/Batch1-chrX_15809051_39911658-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpKRm4Gp/Batch1-chrX_15809051_39911658.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpR2AVdC/Batch1-chr6_0_26032293-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpar4iLh/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr6/Batch1-chr6_0_26032293-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpar4iLh/Batch1-chr6_0_26032293.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp1OaQmQ/Batch1-chr12_0_25362850.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpaGoB8r/Batch1-chrX_15809051_39911658.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpZgOynQ/Batch1-chr1_115252184_150549972.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp9DdWl9/Batch1-chr6_0_26032293.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpcNJ7I5' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr16/Batch1-chr16_67645848_89805966-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpcNJ7I5/Batch1-chr16_67645848_89805966-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpnZ5E5C/Batch1-chrX_123159684_155270560-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp5vaIQa/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chrX/Batch1-chrX_123159684_155270560-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp5vaIQa/Batch1-chrX_123159684_155270560.vcf.gz -O z
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp4UHyuj' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr22/Batch1-chr22_0_22123614-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp4UHyuj/Batch1-chr22_0_22123614-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpzPZGQp/Batch1-chr10_89653776_112327594-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp6LGkEM/Batch1-chrX_123159684_155270560.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpyPbrB6/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr10/Batch1-chr10_89653776_112327594-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpyPbrB6/Batch1-chr10_89653776_112327594.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpqQFyY6/Batch1-chr3_105389071_128200166-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpo7DXGt/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr3/Batch1-chr3_105389071_128200166-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpo7DXGt/Batch1-chr3_105389071_128200166.vcf.gz -O z
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpErHYbJ' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr9/Batch1-chr9_0_21968246-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpErHYbJ/Batch1-chr9_0_21968246-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpqUEfX5/Batch1-chr10_89653776_112327594.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpmIUfrE' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr20/Batch1-chr20_30301091_52185808-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpmIUfrE/Batch1-chr20_30301091_52185808-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpaT4rxj/Batch1-chr3_105389071_128200166.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpmpsOPp' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr4/Batch1-chr4_84384641_106158602-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpmpsOPp/Batch1-chr4_84384641_106158602-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmppNKk5X' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr15/Batch1-chr15_66694266_88420356-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmppNKk5X/Batch1-chr15_66694266_88420356-raw.vcf.gz
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpsxFwJN' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr11/Batch1-chr11_64573101_85956390-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpsxFwJN/Batch1-chr11_64573101_85956390-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpHu1otY/Batch1-chr6_106536070_138192664-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmphOI7zW/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr6/Batch1-chr6_106536070_138192664-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmphOI7zW/Batch1-chr6_106536070_138192664.vcf.gz -O z
> [2017-06-27T15:31Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpFVKN24' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr5/Batch1-chr5_149434794_170815015-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpFVKN24/Batch1-chr5_149434794_170815015-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpbMhQlB/Batch1-chr11_0_22647361-raw.vcf.gz
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpOq8Jqf/Batch1-chr22_0_22123614-raw.vcf.gz
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpzlFh8e/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr11/Batch1-chr11_0_22647361-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpzlFh8e/Batch1-chr11_0_22647361.vcf.gz -O z
> [2017-06-27T15:31Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmprSzI7V/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr22/Batch1-chr22_0_22123614-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmprSzI7V/Batch1-chr22_0_22123614.vcf.gz -O z
> [2017-06-27T15:31Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmppYGeM2/Batch1-chr6_106536070_138192664.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp0Rhp7c/Batch1-chr3_0_30648474-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpBgD_6v/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr3/Batch1-chr3_0_30648474-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpBgD_6v/Batch1-chr3_0_30648474.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpETS7hX/Batch1-chr11_0_22647361.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp03DLof/Batch1-chr22_0_22123614.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp75leqN/Batch1-chr3_0_30648474.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp3fXIAj' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr14/Batch1-chr14_81528486_102548163-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp3fXIAj/Batch1-chr14_81528486_102548163-raw.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpZQjX9F' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr17/Batch1-chr17_17118293_37619375-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpZQjX9F/Batch1-chr17_17118293_37619375-raw.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpUHwtOW' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr12/Batch1-chr12_25368369_46123925-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpUHwtOW/Batch1-chr12_25368369_46123925-raw.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpXehk8h' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr12/Batch1-chr12_112884074_133201585-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpXehk8h/Batch1-chr12_112884074_133201585-raw.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpPai1sE' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr13/Batch1-chr13_28588583_48878190-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpPai1sE/Batch1-chr13_28588583_48878190-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp4mg51a/Batch1-chr15_66694266_88420356-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpqRc2w1/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr15/Batch1-chr15_66694266_88420356-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpqRc2w1/Batch1-chr15_66694266_88420356.vcf.gz -O z
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp1o97Oz' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr5/Batch1-chr5_35860948_56111887-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp1o97Oz/Batch1-chr5_35860948_56111887-raw.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpUq1UPZ' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr2/Batch1-chr2_178097114_198257190-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpUq1UPZ/Batch1-chr2_178097114_198257190-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpusXZgy/Batch1-chr15_66694266_88420356.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpnUIzN8/Batch1-chr4_84384641_106158602-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpLZhakL/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr4/Batch1-chr4_84384641_106158602-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpLZhakL/Batch1-chr4_84384641_106158602.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpBdb4o1/Batch1-chr12_25368369_46123925-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpCQSvLF/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr12/Batch1-chr12_25368369_46123925-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpCQSvLF/Batch1-chr12_25368369_46123925.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp_XOYGg/Batch1-chr4_84384641_106158602.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpLGkm8c/Batch1-chr12_25368369_46123925.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpna7Xeo/Batch1-chr2_16085609_46525081-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpPaQez4/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr2/Batch1-chr2_16085609_46525081-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpPaQez4/Batch1-chr2_16085609_46525081.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpRy0j1_/Batch1-chr2_16085609_46525081.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpljjsfG' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr7/Batch1-chr7_81334700_101459378-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpljjsfG/Batch1-chr7_81334700_101459378-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpF5B1EI/Batch1-chr4_55127256_84384060-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpxxa4hb/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr4/Batch1-chr4_55127256_84384060-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpxxa4hb/Batch1-chr4_55127256_84384060.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpejWCmO/Batch1-chr7_101460614_128829328-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmplrppBC/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr7/Batch1-chr7_101460614_128829328-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmplrppBC/Batch1-chr7_101460614_128829328.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpte1kKS/Batch1-chr1_36932825_65300345-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpwxua1n/Batch1-chr4_55127256_84384060.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpTjLhUm/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr1/Batch1-chr1_36932825_65300345-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpTjLhUm/Batch1-chr1_36932825_65300345.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpO77IiM/Batch1-chr7_101460614_128829328.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpYUVcuc' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr5/Batch1-chr5_112090582_131893150-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpYUVcuc/Batch1-chr5_112090582_131893150-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpq0YjXx/Batch1-chr1_36932825_65300345.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp56Z2P9' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr7/Batch1-chr7_128843219_148504803-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp56Z2P9/Batch1-chr7_128843219_148504803-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpGoJDzp/Batch1-chr10_112328690_135534747-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpscRvlh/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr10/Batch1-chr10_112328690_135534747-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpscRvlh/Batch1-chr10_112328690_135534747.vcf.gz -O z
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpxCnUB8' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr1/Batch1-chr1_17349097_36932514-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpxCnUB8/Batch1-chr1_17349097_36932514-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpgwEOiD/Batch1-chr10_112328690_135534747.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp9OSAq8/Batch1-chr2_178097114_198257190-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpFlC9Zx/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr2/Batch1-chr2_178097114_198257190-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpFlC9Zx/Batch1-chr2_178097114_198257190.vcf.gz -O z
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpHBQpOV' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr22/Batch1-chr22_22127156_41489107-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpHBQpOV/Batch1-chr22_22127156_41489107-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpjVnIEF/Batch1-chr5_35860948_56111887-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpCkrDl3/Batch1-chr2_178097114_198257190.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpGll0eL/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr5/Batch1-chr5_35860948_56111887-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpGll0eL/Batch1-chr5_35860948_56111887.vcf.gz -O z
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpRE0OJZ' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr3/Batch1-chr3_69812987_89156991-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpRE0OJZ/Batch1-chr3_69812987_89156991-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpdPpPb6/Batch1-chrX_100608176_123156526-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmph5SdyF/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chrX/Batch1-chrX_100608176_123156526-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmph5SdyF/Batch1-chrX_100608176_123156526.vcf.gz -O z
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp7Gdk9z' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr3/Batch1-chr3_178917472_198022430-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp7Gdk9z/Batch1-chr3_178917472_198022430-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpXD_XB0/Batch1-chr5_35860948_56111887.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp_Gfxhu/Batch1-chrX_100608176_123156526.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpBz8HYu' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr6/Batch1-chr6_138195976_157100610-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpBz8HYu/Batch1-chr6_138195976_157100610-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpuwL78t/Batch1-chrX_39913133_63406059-raw.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpkb7SEk' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr17/Batch1-chr17_37627126_56432352-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpkb7SEk/Batch1-chr17_37627126_56432352-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmptLdQi4/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chrX/Batch1-chrX_39913133_63406059-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmptLdQi4/Batch1-chrX_39913133_63406059.vcf.gz -O z
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpCUEX0A' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr18/Batch1-chr18_42449189_60795997-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpCUEX0A/Batch1-chr18_42449189_60795997-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpm0kBXu/Batch1-chrX_39913133_63406059.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpnvPsd7' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr17/Batch1-chr17_56434823_74732551-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpnvPsd7/Batch1-chr17_56434823_74732551-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpq0_l8Y/Batch1-chr16_0_23614995-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpIymD_1/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr16/Batch1-chr16_0_23614995-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpIymD_1/Batch1-chr16_0_23614995.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpeX2q2s/Batch1-chr16_67645848_89805966-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpIM12vm/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr16/Batch1-chr16_67645848_89805966-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpIM12vm/Batch1-chr16_67645848_89805966.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpKsSEeI/Batch1-chr16_0_23614995.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpPBxdQo/Batch1-chr16_67645848_89805966.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpp9OEk6/Batch1-chr3_69812987_89156991-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp4L5kGM/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr3/Batch1-chr3_69812987_89156991-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp4L5kGM/Batch1-chr3_69812987_89156991.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpbr8B3k/Batch1-chr3_69812987_89156991.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpkS9stL/Batch1-chr9_0_21968246-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpjP8OiY/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr9/Batch1-chr9_0_21968246-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpjP8OiY/Batch1-chr9_0_21968246.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpczzuiz/Batch1-chr3_47059122_69788857-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmprUGtQQ/Batch1-chr9_0_21968246.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmplUn4Vs/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr3/Batch1-chr3_47059122_69788857-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmplUn4Vs/Batch1-chr3_47059122_69788857.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp2y52VV/Batch1-chr11_64573101_85956390-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpj0A1bv/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr11/Batch1-chr11_64573101_85956390-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpj0A1bv/Batch1-chr11_64573101_85956390.vcf.gz -O z
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpwEQ95v' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr19/Batch1-chr19_0_17937724-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpwEQ95v/Batch1-chr19_0_17937724-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpNT0N9T/Batch1-chr3_47059122_69788857.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpmYxTS8/Batch1-chr11_64573101_85956390.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp_NZNZe' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr9/Batch1-chr9_80343424_97864137-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp_NZNZe/Batch1-chr9_80343424_97864137-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp9C6xbO/Batch1-chr12_46124994_69202276-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpZl7pew/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr12/Batch1-chr12_46124994_69202276-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpZl7pew/Batch1-chr12_46124994_69202276.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpjLMXzF/Batch1-chr5_149434794_170815015-raw.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpMkmXkq' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr5/Batch1-chr5_131894970_149433998-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpMkmXkq/Batch1-chr5_131894970_149433998-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpkvGsS3/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr5/Batch1-chr5_149434794_170815015-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpkvGsS3/Batch1-chr5_149434794_170815015.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpFARUqw/Batch1-chr12_46124994_69202276.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpDOB4DR' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr1/Batch1-chr1_0_17345458-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpDOB4DR/Batch1-chr1_0_17345458-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpjyE5Di/Batch1-chr5_149434794_170815015.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpRZEd4g/Batch1-chr14_81528486_102548163-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp9vdJSE/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr14/Batch1-chr14_81528486_102548163-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp9vdJSE/Batch1-chr14_81528486_102548163.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpcmiG4s/Batch1-chr20_30301091_52185808-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpH3KCeI/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr20/Batch1-chr20_30301091_52185808-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpH3KCeI/Batch1-chr20_30301091_52185808.vcf.gz -O z
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp51CG1v' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr17/Batch1-chr17_0_17117175-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp51CG1v/Batch1-chr17_0_17117175-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpzHwozz/Batch1-chr12_112884074_133201585-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpeQ8DCZ/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr12/Batch1-chr12_112884074_133201585-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpeQ8DCZ/Batch1-chr12_112884074_133201585.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpgeDisN/Batch1-chr20_30301091_52185808.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpQt8_9b/Batch1-chr14_81528486_102548163.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpJWv3fM' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr18/Batch1-chr18_60969985_78077248-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpJWv3fM/Batch1-chr18_60969985_78077248-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpSGm9gl/Batch1-chr12_112884074_133201585.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpQEPjNE' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr16/Batch1-chr16_50785509_67645521-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpQEPjNE/Batch1-chr16_50785509_67645521-raw.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpKi0Ebv' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr11/Batch1-chr11_118339484_135006516-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpKi0Ebv/Batch1-chr11_118339484_135006516-raw.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpzmNtiq' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr19/Batch1-chr19_36208915_52693432-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpzmNtiq/Batch1-chr19_36208915_52693432-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpPxcoMq/Batch1-chr17_17118293_37619375-raw.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpS0nfeG' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr11/Batch1-chr11_85961332_102196301-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpS0nfeG/Batch1-chr11_85961332_102196301-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpKcl4H3/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr17/Batch1-chr17_17118293_37619375-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpKcl4H3/Batch1-chr17_17118293_37619375.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpFsLF3Y/Batch1-chr18_60969985_78077248-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp3Dv1x6/Batch1-chr9_80343424_97864137-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpVn3bOm/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr18/Batch1-chr18_60969985_78077248-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpVn3bOm/Batch1-chr18_60969985_78077248.vcf.gz -O z
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpUYckEz' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr3/Batch1-chr3_89176353_105378078-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpUYckEz/Batch1-chr3_89176353_105378078-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp694Cn8/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr9/Batch1-chr9_80343424_97864137-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp694Cn8/Batch1-chr9_80343424_97864137.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp6uhe9h/Batch1-chr18_60969985_78077248.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp0QCEea' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr3/Batch1-chr3_30664685_47058749-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp0QCEea/Batch1-chr3_30664685_47058749-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmptcJP7B/Batch1-chr17_17118293_37619375.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpCPrYpL/Batch1-chr9_80343424_97864137.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpZHBkP8/Batch1-chr13_28588583_48878190-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpOD_tQs/Batch1-chr7_81334700_101459378-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmppMltUi/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr13/Batch1-chr13_28588583_48878190-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmppMltUi/Batch1-chr13_28588583_48878190.vcf.gz -O z
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpPW96LT/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr7/Batch1-chr7_81334700_101459378-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpPW96LT/Batch1-chr7_81334700_101459378.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp5R5Tcr/Batch1-chr13_28588583_48878190.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmprnkwAU/Batch1-chr7_81334700_101459378.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp_mal5j/Batch1-chr7_128843219_148504803-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpLPyozl/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr7/Batch1-chr7_128843219_148504803-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpLPyozl/Batch1-chr7_128843219_148504803.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpGRmCmZ/Batch1-chr7_128843219_148504803.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp0ENGVf/Batch1-chr5_112090582_131893150-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpTCQMiO/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr5/Batch1-chr5_112090582_131893150-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpTCQMiO/Batch1-chr5_112090582_131893150.vcf.gz -O z
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpIAjjpw' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr2/Batch1-chr2_0_16082981-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpIAjjpw/Batch1-chr2_0_16082981-raw.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp0ATYxa' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr19/Batch1-chr19_17940911_33793325-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp0ATYxa/Batch1-chr19_17940911_33793325-raw.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp1pZP0b' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr11/Batch1-chr11_102198777_118307664-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp1pZP0b/Batch1-chr11_102198777_118307664-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpl4GowR/Batch1-chr5_112090582_131893150.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpQ29MEo' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr1/Batch1-chr1_226253351_242013893-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpQ29MEo/Batch1-chr1_226253351_242013893-raw.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpuXP1KD' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chrX/Batch1-chrX_0_15808664-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpuXP1KD/Batch1-chrX_0_15808664-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp_x5diO/Batch1-chr3_178917472_198022430-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpbfaYXC/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr3/Batch1-chr3_178917472_198022430-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpbfaYXC/Batch1-chr3_178917472_198022430.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpiar8Yq/Batch1-chr1_17349097_36932514-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp_bprtc/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr1/Batch1-chr1_17349097_36932514-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp_bprtc/Batch1-chr1_17349097_36932514.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp20IfnG/Batch1-chr3_89176353_105378078-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpaLFO_9/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr3/Batch1-chr3_89176353_105378078-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpaLFO_9/Batch1-chr3_89176353_105378078.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp__Q912/Batch1-chr3_178917472_198022430.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpP19JQ9/Batch1-chr1_17349097_36932514.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpodlJKy/Batch1-chr22_22127156_41489107-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpvpkGcV/Batch1-chr6_138195976_157100610-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpjEwgoo/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr22/Batch1-chr22_22127156_41489107-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpjEwgoo/Batch1-chr22_22127156_41489107.vcf.gz -O z
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpZrGByu' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr15/Batch1-chr15_88423495_102531392-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpZrGByu/Batch1-chr15_88423495_102531392-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp67FND_/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr6/Batch1-chr6_138195976_157100610-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp67FND_/Batch1-chr6_138195976_157100610.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp2obK27/Batch1-chr3_89176353_105378078.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpSEw5nK/Batch1-chr2_0_16082981-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpw_0JZ6/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr2/Batch1-chr2_0_16082981-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpw_0JZ6/Batch1-chr2_0_16082981.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp6f19RZ/Batch1-chr22_22127156_41489107.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpkFNRNz/Batch1-chr6_138195976_157100610.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpGdtaPc' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr6/Batch1-chr6_157150355_171115067-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpGdtaPc/Batch1-chr6_157150355_171115067-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp8LB74d/Batch1-chr2_0_16082981.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpNsNOUf/Batch1-chrX_0_15808664-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp56itKv/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chrX/Batch1-chrX_0_15808664-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp56itKv/Batch1-chrX_0_15808664.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpseYzOi/Batch1-chrX_0_15808664.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpLxuJaH' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr21/Batch1-chr21_36171592_48129895-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpLxuJaH/Batch1-chr21_36171592_48129895-raw.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp0VzCR7' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr20/Batch1-chr20_52188277_63025520-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp0VzCR7/Batch1-chr20_52188277_63025520-raw.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp5eSmSp' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr7/Batch1-chr7_148506157_159138663-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp5eSmSp/Batch1-chr7_148506157_159138663-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpx5VYmD/Batch1-chr18_42449189_60795997-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpbI1vth/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr18/Batch1-chr18_42449189_60795997-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpbI1vth/Batch1-chr18_42449189_60795997.vcf.gz -O z
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpB9HJn2' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr22/Batch1-chr22_41513185_51304566-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpB9HJn2/Batch1-chr22_41513185_51304566-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp1nQ7ah/Batch1-chr18_42449189_60795997.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp9ekSyW' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr5/Batch1-chr5_170817049_180915260-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp9ekSyW/Batch1-chr5_170817049_180915260-raw.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpDcMth_' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr9/Batch1-chr9_133710828_141213431-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpDcMth_/Batch1-chr9_133710828_141213431-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpvUBn7u/Batch1-chr1_226253351_242013893-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpkaKnVY/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr1/Batch1-chr1_226253351_242013893-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpkaKnVY/Batch1-chr1_226253351_242013893.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpi5vxRJ/Batch1-chr17_56434823_74732551-raw.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpQ79jj2' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr1/Batch1-chr1_242015588_249250621-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpQ79jj2/Batch1-chr1_242015588_249250621-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpFjMB8k/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr17/Batch1-chr17_56434823_74732551-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpFjMB8k/Batch1-chr17_56434823_74732551.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpod9TXQ/Batch1-chr17_56434823_74732551.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpYJiGut/Batch1-chr1_226253351_242013893.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp9G9kl0' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr17/Batch1-chr17_74732875_81195210-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp9G9kl0/Batch1-chr17_74732875_81195210-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpax7Nhu/Batch1-chr17_0_17117175-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpQM9Bte/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr17/Batch1-chr17_0_17117175-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpQM9Bte/Batch1-chr17_0_17117175.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp_HvH1L/Batch1-chr5_131894970_149433998-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmprX8pwJ/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr5/Batch1-chr5_131894970_149433998-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmprX8pwJ/Batch1-chr5_131894970_149433998.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpBMHjI6/Batch1-chr17_0_17117175.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp0ilavX/Batch1-chr16_50785509_67645521-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpqLkZJg/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr16/Batch1-chr16_50785509_67645521-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpqLkZJg/Batch1-chr16_50785509_67645521.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpVv2YWr/Batch1-chr5_131894970_149433998.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp0hPcuA' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr14/Batch1-chr14_102548442_107349540-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp0hPcuA/Batch1-chr14_102548442_107349540-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpUuueWz/Batch1-chr16_50785509_67645521.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpNvmTfQ/Batch1-chr17_37627126_56432352-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpqfjM0O/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr17/Batch1-chr17_37627126_56432352-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpqfjM0O/Batch1-chr17_37627126_56432352.vcf.gz -O z
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpLxoR4Y' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr19/Batch1-chr19_52705191_59128983-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpLxoR4Y/Batch1-chr19_52705191_59128983-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpWqze6x/Batch1-chr1_0_17345458-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpYlyezy/Batch1-chr17_37627126_56432352.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpPoojOr/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr1/Batch1-chr1_0_17345458-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpPoojOr/Batch1-chr1_0_17345458.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmppYLhWx/Batch1-chr1_0_17345458.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp1aqSal' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr12/Batch1-chr12_133202225_133851895-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp1aqSal/Batch1-chr12_133202225_133851895-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpNWv4sY/Batch1-chr17_74732875_81195210-raw.vcf.gz
> [2017-06-27T15:32Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx7500m -XX:+UseSerialGC -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpwY7DEo' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.01 -N NTP17-002714_annotated_R1 -b /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /isilon/scratch/NS-JeffTest4/work/vardict/chr16/Batch1-chr16_89806292_90354753-unmerged-regions-nolcr-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -A -N NTP17-002714_annotated_R1 -E -f 0.01 | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa")' | bcftools filter -i 'QUAL >= 0' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/share/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpwY7DEo/Batch1-chr16_89806292_90354753-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpUMcsp8/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr17/Batch1-chr17_74732875_81195210-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpUMcsp8/Batch1-chr17_74732875_81195210.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp5Kb7Gj/Batch1-chr11_85961332_102196301-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmptFyUZZ/Batch1-chr1_242015588_249250621-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpwD4k8R/Batch1-chr17_74732875_81195210.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpWQxVXA/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr11/Batch1-chr11_85961332_102196301-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpWQxVXA/Batch1-chr11_85961332_102196301.vcf.gz -O z
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpBHIyLS/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr1/Batch1-chr1_242015588_249250621-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpBHIyLS/Batch1-chr1_242015588_249250621.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpge6Wvr/Batch1-chr11_85961332_102196301.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp8hKnJN/Batch1-chr1_242015588_249250621.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmph_jwJD/Batch1-chr3_30664685_47058749-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpPSI6E9/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr3/Batch1-chr3_30664685_47058749-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpPSI6E9/Batch1-chr3_30664685_47058749.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpabPp8w/Batch1-chr3_30664685_47058749.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpLf1hE0/Batch1-chr11_118339484_135006516-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp7TSQim/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr11/Batch1-chr11_118339484_135006516-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp7TSQim/Batch1-chr11_118339484_135006516.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpmeRPtD/Batch1-chr11_118339484_135006516.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp8ajYK9/Batch1-chr19_36208915_52693432-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpDnVUnS/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr19/Batch1-chr19_36208915_52693432-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpDnVUnS/Batch1-chr19_36208915_52693432.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpvT_Qh6/Batch1-chr19_36208915_52693432.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp1Iql4g/Batch1-chr19_17940911_33793325-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpv2FDhe/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr19/Batch1-chr19_17940911_33793325-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpv2FDhe/Batch1-chr19_17940911_33793325.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpWagAcT/Batch1-chr19_17940911_33793325.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpE9DB_W/Batch1-chr19_0_17937724-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpbP2FEg/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr19/Batch1-chr19_0_17937724-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpbP2FEg/Batch1-chr19_0_17937724.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpK3S1Dc/Batch1-chr6_157150355_171115067-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpLLB1Ay/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr6/Batch1-chr6_157150355_171115067-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpLLB1Ay/Batch1-chr6_157150355_171115067.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpqsx_Oo/Batch1-chr19_0_17937724.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpvjibEq/Batch1-chr11_102198777_118307664-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpII7sH6/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr11/Batch1-chr11_102198777_118307664-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpII7sH6/Batch1-chr11_102198777_118307664.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpV9P1wm/Batch1-chr6_157150355_171115067.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpVxBT9R/Batch1-chr21_36171592_48129895-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpwSldbd/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr21/Batch1-chr21_36171592_48129895-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpwSldbd/Batch1-chr21_36171592_48129895.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpVSH_sB/Batch1-chr11_102198777_118307664.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpHZRY1J/Batch1-chr21_36171592_48129895.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpLWEcF4/Batch1-chr15_88423495_102531392-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpVDLjLn/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr15/Batch1-chr15_88423495_102531392-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpVDLjLn/Batch1-chr15_88423495_102531392.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpKVOQrx/Batch1-chr15_88423495_102531392.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpqCmtOW/Batch1-chr20_52188277_63025520-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpeUpId_/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr20/Batch1-chr20_52188277_63025520-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpeUpId_/Batch1-chr20_52188277_63025520.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpmrTv7D/Batch1-chr9_133710828_141213431-raw.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpKhQy1U/Batch1-chr20_52188277_63025520.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpWFZbYV/Batch1-chr22_41513185_51304566-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpzroq_6/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr9/Batch1-chr9_133710828_141213431-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpzroq_6/Batch1-chr9_133710828_141213431.vcf.gz -O z
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpj8IsZe/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr22/Batch1-chr22_41513185_51304566-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpj8IsZe/Batch1-chr22_41513185_51304566.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmphMUw8J/Batch1-chr7_148506157_159138663-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpERCGcw/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr7/Batch1-chr7_148506157_159138663-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpERCGcw/Batch1-chr7_148506157_159138663.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpIJrtaj/Batch1-chr9_133710828_141213431.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpA3Pccg/Batch1-chr22_41513185_51304566.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpspTKk1/Batch1-chr7_148506157_159138663.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpGx6Ndr/Batch1-chr16_89806292_90354753-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp_Fgejj/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr16/Batch1-chr16_89806292_90354753-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp_Fgejj/Batch1-chr16_89806292_90354753.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpbTr31k/Batch1-chr19_52705191_59128983-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpdgkZuR/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr19/Batch1-chr19_52705191_59128983-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpdgkZuR/Batch1-chr19_52705191_59128983.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpX8NEwH/Batch1-chr16_89806292_90354753.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpE6uJog/Batch1-chr12_133202225_133851895-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpaafQdR/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr12/Batch1-chr12_133202225_133851895-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpaafQdR/Batch1-chr12_133202225_133851895.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpnv2Opa/Batch1-chr5_170817049_180915260-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpPP8GDQ/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr5/Batch1-chr5_170817049_180915260-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpPP8GDQ/Batch1-chr5_170817049_180915260.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpPk1_BU/Batch1-chr19_52705191_59128983.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpO5stMq/Batch1-chr12_133202225_133851895.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpGEFPPN/Batch1-chr5_170817049_180915260.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp1gaCvi/Batch1-chr14_102548442_107349540-raw.vcf.gz
> [2017-06-27T15:32Z] vcfanno /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpaeQo_B/dbsnp.conf /isilon/scratch/NS-JeffTest4/work/vardict/chr14/Batch1-chr14_102548442_107349540-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpaeQo_B/Batch1-chr14_102548442_107349540.vcf.gz -O z
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpL2euQ1/Batch1-chr14_102548442_107349540.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/bcftools concat --naive -O z --file-list /isilon/scratch/NS-JeffTest4/work/vardict/Batch1-files.list -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpDH8de0/Batch1.vcf.gz
> [2017-06-27T15:32Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpQH4EV4/Batch1.vcf.gz
> [2017-06-27T15:32Z] export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && /usr/local/share/bcbio/anaconda/bin/snpEff -Xms750m -Xmx88g -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpNRnzZJ/tmp eff -dataDir /usr/local/share/bcbio/genomes/Hsapiens/hg19/snpeff -hgvs -cancer -canon -noLog -i vcf -o vcf -csvStats /isilon/scratch/NS-JeffTest4/work/vardict/Batch1-effects-stats.csv -s /isilon/scratch/NS-JeffTest4/work/vardict/Batch1-effects-stats.html GRCh37.75 /isilon/scratch/NS-JeffTest4/work/vardict/Batch1.vcf.gz | /usr/local/share/bcbio/anaconda/bin/bgzip --threads 16 -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpNRnzZJ/Batch1-effects.vcf.gz
> [2017-06-27T15:34Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpkzM8bd/Batch1-effects.vcf.gz
> [2017-06-27T15:34Z] bcftools reheader -h /isilon/scratch/NS-JeffTest4/work/vardict/Batch1-effects-annotated-header.txt /isilon/scratch/NS-JeffTest4/work/vardict/Batch1-effects.vcf.gz | bcftools view | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpISfgcb/Batch1-effects-annotated.vcf.gz
> [2017-06-27T15:34Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpdM5CSN/Batch1-effects-annotated.vcf.gz
> [2017-06-27T15:34Z] export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && /usr/local/share/bcbio/anaconda/bin/gemini load --passonly --skip-cadd --skip-gerp-bp -v /isilon/scratch/NS-JeffTest4/work/vardict/Batch1-effects-annotated.vcf.gz -t snpEff --cores 16 --tempdir /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpajKkpr /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpajKkpr/Batch1-effects-annotated.db
> [2017-06-27T15:35Z] cat /isilon/scratch/NS-JeffTest4/work/vardict/Batch1-effects-annotated-priority.tsv | /usr/local/share/bcbio/anaconda/bin/bgzip --threads 16 -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpvLjsSQ/Batch1-effects-annotated-priority.tsv.gz
> [2017-06-27T15:35Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -0 -c '#' -s 1 -b 2 -e 3 /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpprHPJI/Batch1-effects-annotated-priority.tsv.gz
> [2017-06-27T15:35Z] bcftools annotate -a /isilon/scratch/NS-JeffTest4/work/vardict/Batch1-effects-annotated-priority.tsv.gz -h /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpUrxBDs/Batch1-effects-annotated-priority-repeatheader.txt -c CHROM,FROM,TO,REF,ALT,INFO/EPR /isilon/scratch/NS-JeffTest4/work/vardict/Batch1-effects-annotated.vcf.gz | bcftools filter -m '+' -s 'LowPriority' -e "EPR[*] != 'pass'" | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpUrxBDs/Batch1-effects-annotated-priority.vcf.gz
> [2017-06-27T15:35Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp2U83w0/Batch1-effects-annotated-priority.vcf.gz
> [2017-06-27T15:35Z] cat /isilon/scratch/NS-JeffTest4/work/vardict/Batch1-effects-annotated-priority-germline.vcf | /usr/local/share/bcbio/anaconda/bin/bgzip --threads 16 -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpjiDpIK/Batch1-effects-annotated-priority-germline.vcf.gz
> [2017-06-27T15:35Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpnsRGQE/Batch1-effects-annotated-priority-germline.vcf.gz
> [2017-06-27T15:35Z] gunzip -c /isilon/scratch/NS-JeffTest4/work/gemini/Batch1-vardict.vcf.gz | sed 's/ID=AD,Number=./ID=AD,Number=R/' | vt decompose -s - | vt normalize -n -r /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa - | awk '{ gsub("./-65", "./."); print $0 }'| bcftools view -f 'PASS,.' | sed -e 's/Number=A/Number=1/g' | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpP0VcCX/Batch1-vardict-decompose.vcf.gz
> [2017-06-27T15:35Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpn46fFG/Batch1-vardict-decompose.vcf.gz
> [2017-06-27T15:35Z] export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && /usr/local/share/bcbio/anaconda/bin/snpEff -Xms750m -Xmx88g -Djava.io.tmpdir=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpv7lKzE/tmp eff -dataDir /usr/local/share/bcbio/genomes/Hsapiens/hg19/snpeff -hgvs -cancer -canon -noLog -i vcf -o vcf -csvStats /isilon/scratch/NS-JeffTest4/work/gemini/Batch1-vardict-decompose-effects-stats.csv -s /isilon/scratch/NS-JeffTest4/work/gemini/Batch1-vardict-decompose-effects-stats.html GRCh37.75 /isilon/scratch/NS-JeffTest4/work/gemini/Batch1-vardict-decompose.vcf.gz | /usr/local/share/bcbio/anaconda/bin/bgzip --threads 16 -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpv7lKzE/Batch1-vardict-decompose-effects.vcf.gz
> [2017-06-27T15:37Z] /usr/local/share/bcbio/anaconda/bin/tabix -f -p vcf /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpOevw7v/Batch1-vardict-decompose-effects.vcf.gz
> [2017-06-27T15:37Z] /usr/local/share/bcbio/anaconda/bin/vcfanno -p 16 -lua /usr/local/share/bcbio/genomes/Hsapiens/hg19/config/vcfanno/gemini.lua -base-path /usr/local/share/bcbio/gemini_data /usr/local/share/bcbio/genomes/Hsapiens/hg19/config/vcfanno/gemini.conf /isilon/scratch/NS-JeffTest4/work/gemini/Batch1-vardict-decompose-effects.vcf.gz | sed -e 's/Number=A/Number=1/g' | bgzip -c > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpnf1pmv/Batch1-vardict-decompose-effects-annotated-gemini.vcf.gz
> [2017-06-27T15:37Z] export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && /usr/local/share/bcbio/anaconda/bin/gemini load --passonly --skip-cadd --skip-gerp-bp -v /isilon/scratch/NS-JeffTest4/work/gemini/Batch1-vardict-decompose-effects-annotated-gemini.vcf.gz -t snpEff --cores 16 --tempdir /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp6I3b2Z /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp6I3b2Z/Batch1-vardict.db
> [2017-06-27T15:38Z] /usr/local/share/bcbio/anaconda/bin/gemini amend --sample /isilon/scratch/NS-JeffTest4/work/gemini/Batch1-vardict-decompose-effects-annotated-gemini.ped /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp6I3b2Z/Batch1-vardict.db
> [2017-06-27T15:38Z] export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && /usr/local/share/bcbio/anaconda/bin/fastqc -d /isilon/scratch/NS-JeffTest4/work/qc/NTP17-002714_annotated_R1/bcbiotx/tmpX54gHS -t 16 --extract -o /isilon/scratch/NS-JeffTest4/work/qc/NTP17-002714_annotated_R1/bcbiotx/tmpX54gHS -f bam /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam
> [2017-06-27T15:39Z] /usr/local/share/bcbio/anaconda/bin/samtools stats /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmppmXTUr/NTP17-002714_annotated_R1.txt
> [2017-06-27T15:40Z] /usr/local/share/bcbio/anaconda/bin/samtools stats /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp5EnbPh/NTP17-002714_annotated_R1.txt
> [2017-06-27T15:40Z] bedtools slop -i /isilon/scratch/NS-JeffTest4/work/bedprep/DHS-3501Z.roi-merged.bed -g /usr/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa.fai -b 200 > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpMP9eWQ/DHS-3501Z.roi-merged-padded.bed
> [2017-06-27T15:40Z] /usr/local/share/bcbio/anaconda/bin/sambamba view -c -t 1 /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam -L /isilon/scratch/NS-JeffTest4/work/qc/NTP17-002714_annotated_R1/coverage/DHS-3501Z.roi-merged-padded.bed -F "not unmapped and not mate_is_unmapped and not secondary_alignment and not failed_quality_control and not duplicate" > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp7Vs_qP/num_not_unmapped_and_not_mate_is_unmapped_and_not_secondary_alignment_and_not_failed_quality_control_and_not_duplicate_on_variant_regions_padded
> [2017-06-27T15:40Z] /usr/local/share/bcbio/anaconda/bin/bcftools stats -s NTP17-002714_annotated_R1 -f PASS /isilon/scratch/NS-JeffTest4/work/vardict/Batch1-effects-annotated-priority.vcf.gz > /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmp6SmRpI/orig_NTP17-002714_annotated_R1_bcftools_stats.txt
> [2017-06-27T15:40Z] samtools view -u -f 4 /isilon/scratch/NS-JeffTest4/work/align/NTP17-002714_annotated_R1/NTP17-002714_annotated_R1-sort.bam | bamtofastq collate=0 | bwa mem -t 16 /usr/local/share/bcbio/genomes/Hsapiens/hg19/viral/gdc-viral.fa - | bamsort tmpfile=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpSx3pcn/NTP17-002714_annotated_R1-gdc-viral-tmp inputthreads=16 outputthreads=16 inputformat=sam index=1 indexfilename=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpSx3pcn/NTP17-002714_annotated_R1-gdc-viral.bam.bai O=/isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpSx3pcn/NTP17-002714_annotated_R1-gdc-viral.bam
> [2017-06-27T15:41Z] export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && /usr/local/share/bcbio/anaconda/bin/multiqc -f -l /isilon/scratch/NS-JeffTest4/work/qc/multiqc/list_files.txt -o /isilon/scratch/NS-JeffTest4/work/bcbiotx/tmpi2BWmi
Jeffrey Day
Jun 28, 2017, 12:35:08 PM6/28/17
to biovalidation, funar...@gmail.com, luca.b...@marionegri.it, jeffre...@gmail.com, vfu...@neogenomics.com
Hey Brad,
I first want to say thanks for all of your help with this issue. I finally corrected the YAML file to have umi_type: fastq_name. Upon me doing this, it gave me the same error I was receiving when trying to run fgbio standalone. The error stated this exactly:
Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 249439, Read name M00210:23:000000000-B32K3:1:2103:25514:8599 :UMI_CGCTGGGTTGGGGCCTC, Zero-length read without FZ, CS or CQ tag
I have tried to trouble shoot this error on the stand alone application and was not successful. I was wondering do you know a way to get around this issue. Thanks again for all of your help and I hope you have a blessed day.
Humbly,
Jeffrey Day
> [2017-06-27T15:31Z] vcfanno /is...
Vincent Funari
Jun 28, 2017, 7:14:51 PM6/28/17
to biovalidation, funar...@gmail.com, luca.b...@marionegri.it, jeffre...@gmail.com, vfu...@neogenomics.com
Thanks Brad for your help,
Not using the path worked perfectly, and its now starting to call the fgbio app, it wasnt intuitive for me that it works with just the name of the file(no need for path), and your right it is much more straight forward that way.
We found another error jeff has is now due reads that were cleaned in prep but never filtered out. So, we are now going back and removing those empty reads. We will let you know after we do that. If we clean this it will be great for tumor variant calling!
Best
> [2017-06-27T15:31Z] vcfanno /is...
Brad Chapman
Jun 29, 2017, 2:52:42 PM6/29/17
to Vincent Funari, biovalidation, funar...@gmail.com, luca.b...@marionegri.it, jeffre...@gmail.com, vfu...@neogenomics.com
Vincent and Jeffrey;
Thanks for following up. I'm glad this worked and that you tracked down the
empty read issue causing fgbio to fail. Hope all works cleanly now and you get
some improved variant calls with the consensus barcodes. Thanks again,
Brad
> [ text/plain ]
>> > To post to this group, send email to bioval...@googlegroups.com
>> <javascript:>.
Vincent Funari
Jun 29, 2017, 8:00:13 PM6/29/17
to biovalidation, funar...@gmail.com, luca.b...@marionegri.it, jeffre...@gmail.com, vfu...@neogenomics.com
Hi Brad/Luca
The good news is that we got past the group by UMIs feature in the app working great, and all the way to CallMolecularConsensus Reads! The bad news is it looks like the fgbio app is sensitive to the UMI length!
So it cant compare 2 UMIs that are of unequal length at the position. And thats a problem because on of the UMIs is on the 3' side of the Read 1, so sometimes it is truncated ( because of the length of the read). So the whole app errors out because the UMIs are different lengths.
If anyone has any suggestions to get around this we are open.
[2017/06/29 16:44:25 | GroupReadsByUmi | Info] Sorted 5,000,000 record. Elapsed time: 00:00:43s. Time for last 1,000,000: 8s. Last read position: chr20:57,480,425
[2017/06/29 16:44:28 | GroupReadsByUmi | Info] Assigning reads to UMIs and outputting.
[2017/06/29 16:44:30 | FgBioMain | Info] GroupReadsByUmi failed. Elapsed time: 0.86 minutes.
Exception in thread "main" java.lang.IllegalArgumentException: requirement failed: Cannot count mismatches in strings of differing lengths: CAAAACTGTCAATTGACA TTGCAAGAGTGATCA
Brad Chapman
Jun 29, 2017, 8:52:43 PM6/29/17
to Vincent Funari, biovalidation, funar...@gmail.com, luca.b...@marionegri.it, jeffre...@gmail.com, vfu...@neogenomics.com
Vincent;
Thanks for the update. I suspect you'll have to do some kind of processing of
UMIs to give identical tags to be able to use the fgbio algorithms. I'm not an
expert on all the details and would suggest asking about this on the fgbio
issue tracker:
https://github.com/fulcrumgenomics/fgbio/issues
Tim and Nils are very responsive and can hopefully help with suggestions,
Brad
> [ text/plain ]
Vincent Funari
Jun 30, 2017, 6:58:14 PM6/30/17
to biovalidation, funar...@gmail.com, luca.b...@marionegri.it, jeffre...@gmail.com, vfu...@neogenomics.com
Ok
I found a work around by adding Ns to complete the partial UMI.
It finsihed without error
so now we just have to see if that helps sensitivity/noise with some testing,
In mean time I also posted that error to the fgbio forum.
Thanks for all the help
Luca Beltrame
Oct 9, 2017, 7:32:41 AM10/9/17
to Vincent Funari, biovalidation, jeffre...@gmail.com, vfu...@neogenomics.com
In data sabato 1 luglio 2017 00:58:14 CEST, Vincent Funari ha scritto:
Hello Vincent,
> In mean time I also posted that error to the fgbio forum.
> Thanks for all the help
I realize this was posted several months ago, but I read in the thread that
you managed to process the data in a format amenable to bcbio to handle UMIs
(fgbio problem notwithstanding).
Would you be able to share at least the high level steps for this procedure?
As I'm about to process a large number of samples with UMIs, it would be very
useful.
Thanks.
Hello Vincent,
> In mean time I also posted that error to the fgbio forum.
> Thanks for all the help
you managed to process the data in a format amenable to bcbio to handle UMIs
(fgbio problem notwithstanding).
Would you be able to share at least the high level steps for this procedure?
As I'm about to process a large number of samples with UMIs, it would be very
useful.
Thanks.
Luca Beltrame
Oct 9, 2017, 10:52:07 AM10/9/17
to bioval...@googlegroups.com, Vincent Funari, jeffre...@gmail.com, vfu...@neogenomics.com
In data lunedì 9 ottobre 2017 13:32:00 CEST, Luca Beltrame ha scritto:
> As I'm about to process a large number of samples with UMIs, it would be
> very useful.
Ah, I found what I was looking for in the rest of the thread (missed it).
> As I'm about to process a large number of samples with UMIs, it would be
> very useful.
Sorry for the noise, I'll poke if there' s anything unclear.
Luca Beltrame
Oct 12, 2017, 10:13:56 AM10/12/17
to bioval...@googlegroups.com, Vincent Funari, jeffre...@gmail.com, vfu...@neogenomics.com
In data lunedì 9 ottobre 2017 16:52:02 CEST, Luca Beltrame ha scritto:
> Ah, I found what I was looking for in the rest of the thread (missed it).
> Sorry for the noise, I'll poke if there' s anything unclear.
So far I think I "almost" nailed it completely. However I got hit by the issue
> Ah, I found what I was looking for in the rest of the thread (missed it).
> Sorry for the noise, I'll poke if there' s anything unclear.
of differing UMI lengths with fgbio:
Exception in thread "main" java.lang.IllegalArgumentException: requirement
AG
Vincent, what was your approach to workaround this? I padded the UMIs with Ns
before adding them with bcbio_fastq_umi_prep but it doesn't seem it was the
right idea.
Luca Beltrame
Oct 16, 2017, 3:01:53 AM10/16/17
to bioval...@googlegroups.com, Vincent Funari, jeffre...@gmail.com, vfu...@neogenomics.com
In data giovedì 12 ottobre 2017 16:13:48 CEST, Luca Beltrame ha scritto:
> Vincent, what was your approach to workaround this? I padded the UMIs with
> Ns before adding them with bcbio_fastq_umi_prep but it doesn't seem it was
> the right idea.
And it turns out, I fed it the unpadded sequence file: once using the right
> Vincent, what was your approach to workaround this? I padded the UMIs with
> Ns before adding them with bcbio_fastq_umi_prep but it doesn't seem it was
> the right idea.
file, everything works. I'll show myself to the door now. ;)
Luca Beltrame
Oct 16, 2017, 11:32:33 AM10/16/17
to Dr. Vincent Funari, bioval...@googlegroups.com, Vincent Funari, jeffre...@gmail.com
In data lunedì 16 ottobre 2017 17:25:35 CEST, Dr. Vincent Funari ha scritto:
> We always had the error you had unless we padded the UMIs. Im curious how
> you did it without the padding.
I actually padded the file: only, in my tests I picked up the wrong file and
so it didn't work. With a padded file works.
I adapted your workflow, but using atropos (for multicore trimming).
> We always had the error you had unless we padded the UMIs. Im curious how
> you did it without the padding.
I actually padded the file: only, in my tests I picked up the wrong file and
so it didn't work. With a padded file works.
I adapted your workflow, but using atropos (for multicore trimming).
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