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This group provides a forum for questions or discussion related to the
strelka somatic variant caller
.
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Qiaoyan Wang
7/3/19
Q&A
Different --forceGT vcf on the same cram causing different sites calls besides the forceGT sites.
I was running Strelka by using different --forceGT vcf files on the same cram. No doubt, I got all
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Q&A
Different --forceGT vcf on the same cram causing different sites calls besides the forceGT sites.
I was running Strelka by using different --forceGT vcf files on the same cram. No doubt, I got all
7/3/19
Tim Fennell
, …
Andrej Benjak
5
4/16/19
Failure (and simple fix) running against hs38DH due to colons and asterisks in sequence names
Thanks for the fix in the configureStrelkaWorkflow.pl I managed to run Strelka1 by removing all
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Failure (and simple fix) running against hs38DH due to colons and asterisks in sequence names
Thanks for the fix in the configureStrelkaWorkflow.pl I managed to run Strelka1 by removing all
4/16/19
Marina Orlova
4/10/19
Strelka2 training sets
Hello! Which cell lines were used for EVS training?
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Strelka2 training sets
Hello! Which cell lines were used for EVS training?
4/10/19
ANUBHAB KHAN
2/5/19
sample names in output vcf file
Hi, I have used strelka for calling germline variants using BAM files without readgroups. I think
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sample names in output vcf file
Hi, I have used strelka for calling germline variants using BAM files without readgroups. I think
2/5/19
juny...@gmail.com
11/27/18
SomaticEVS threshold
Dear Strelka developers, I use Strelka v2.9.7 to call somatic variants and have a question about EVS
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SomaticEVS threshold
Dear Strelka developers, I use Strelka v2.9.7 to call somatic variants and have a question about EVS
11/27/18
Anju Singhal
10/9/18
having issue reference genome mismatch the length of chromosome chrM is 16569 in the reference fasta
having issue reference genome mismatch the length of chromosome chrM is 16569 in the reference fasta
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having issue reference genome mismatch the length of chromosome chrM is 16569 in the reference fasta
having issue reference genome mismatch the length of chromosome chrM is 16569 in the reference fasta
10/9/18
pinnintil...@gmail.com
,
Saunders, Chris
2
4/20/18
Q&A
Stelka Somatic output
Hi Likith, Thanks for checking. Note this email list is inactive and any current strelka issues
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Q&A
Stelka Somatic output
Hi Likith, Thanks for checking. Note this email list is inactive and any current strelka issues
4/20/18
nick.p...@personalis.com
,
Saunders, Chris
2
2/23/18
Q&A
Troubleshooting Germline Performance
Hi Nick, Sorry for the delay. Note we are better able to support queries through issues filed on the
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Q&A
Troubleshooting Germline Performance
Hi Nick, Sorry for the delay. Note we are better able to support queries through issues filed on the
2/23/18
Michal
, …
Attila Gulyás-Kovács
4
11/22/17
build error with strelka_workflow-1.0.15
Hi Chris, I look forward to using strelka2, which by the way could be installed seamlessly. But I may
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build error with strelka_workflow-1.0.15
Hi Chris, I look forward to using strelka2, which by the way could be installed seamlessly. But I may
11/22/17
Cheng Grace
11/16/17
A dot in ALT
Hello expert, I have used Strelka version 1.0.15 to call SNPs of my exome data. In the output vcf
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A dot in ALT
Hello expert, I have used Strelka version 1.0.15 to call SNPs of my exome data. In the output vcf
11/16/17
sdvie
,
Jingzhong Xie
2
11/13/17
error about genome size / bad lexical cast when using a non-human reference genome
I face the same problem. Any solution for it now? Thanks. Jingzhong On Thursday, July 14, 2016 at 11:
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error about genome size / bad lexical cast when using a non-human reference genome
I face the same problem. Any solution for it now? Thanks. Jingzhong On Thursday, July 14, 2016 at 11:
11/13/17
Fouad Yousif
, …
Chris Saunders
6
10/11/17
Segmentation Fault
Hi Dawn, Our ability to offer continued support for the original strelka release is fairly limited.
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Segmentation Fault
Hi Dawn, Our ability to offer continued support for the original strelka release is fairly limited.
10/11/17
Chris Saunders
9/25/17
Announcement
Strelka2
Strelka2 is now available from: https://github.com/Illumina/strelka This update brings numerous
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Announcement
Strelka2
Strelka2 is now available from: https://github.com/Illumina/strelka This update brings numerous
9/25/17
jane.me...@gmail.com
, …
Mark Cowley
4
8/30/17
Q&A
How to get the normal coverage of the reference allele in all.somatic.indels.vcf file?
Hi Chris, I keep coming back to this old thread when i'm explaining (or reminding myself) what
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Q&A
How to get the normal coverage of the reference allele in all.somatic.indels.vcf file?
Hi Chris, I keep coming back to this old thread when i'm explaining (or reminding myself) what
8/30/17
noe91
8/25/17
indel read count
Hello! I am using Strelka as variant caller for INDELs. I would like to obtain the number of read
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indel read count
Hello! I am using Strelka as variant caller for INDELs. I would like to obtain the number of read
8/25/17
ognjen.m...@sbgenomics.com
7/10/17
Indel metrics
Hi! There are already several posts describing to more or less details the nomenclature with TAR, TIR
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Indel metrics
Hi! There are already several posts describing to more or less details the nomenclature with TAR, TIR
7/10/17
Raymond Lim
,
lwliv...@gmail.com
2
6/19/17
Build error with v1.0.14
Hi Lim, Have you solved this problem? I have encountered the same porblem as you, could you give me
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Build error with v1.0.14
Hi Lim, Have you solved this problem? I have encountered the same porblem as you, could you give me
6/19/17
lwliv...@gmail.com
6/19/17
installing error: /usr/lib/../lib64/crt1.o: undefined reference to `main'
When installing the strelka_workflow-1.0.15, I encountered an problem. make -C lib test make[3]:
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installing error: /usr/lib/../lib64/crt1.o: undefined reference to `main'
When installing the strelka_workflow-1.0.15, I encountered an problem. make -C lib test make[3]:
6/19/17
Christian Rausch
6/8/17
is strelka's extended option --region=REGION appropriate to specify target region for panel or exome
Dear all, * this could decrease the runtime in case of panel / exome sequencing data as only the
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is strelka's extended option --region=REGION appropriate to specify target region for panel or exome
Dear all, * this could decrease the runtime in case of panel / exome sequencing data as only the
6/8/17
Arshi Arora
,
Tyler Funnell
4
5/30/17
Q&A
no somatic calls in output file
Thanks for posting here Tyler! I agree, in my case too something is wrong with the bam. But I do see
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Q&A
no somatic calls in output file
Thanks for posting here Tyler! I agree, in my case too something is wrong with the bam. But I do see
5/30/17
Erich Peterson
5/26/17
Germline SNVs
Hello, I was wondering if Strelka 1 or 2, run in a tumor / normal matched mode, outputs germline
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Germline SNVs
Hello, I was wondering if Strelka 1 or 2, run in a tumor / normal matched mode, outputs germline
5/26/17
Saikat Banerjee
4/19/17
*** target pattern contains no '%'.
Hi everyone, I have generated the Make file. but running sudo make gives me the above mentioned error
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*** target pattern contains no '%'.
Hi everyone, I have generated the Make file. but running sudo make gives me the above mentioned error
4/19/17
Saikat Banerjee
2
4/18/17
error in running the tool.
On Tuesday, April 18, 2017 at 4:56:10 PM UTC+5:30, Saikat Banerjee wrote: hello everyone here, I am
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error in running the tool.
On Tuesday, April 18, 2017 at 4:56:10 PM UTC+5:30, Saikat Banerjee wrote: hello everyone here, I am
4/18/17
CA
4/18/17
WGS segmentation fault
Hello, I'm having some issues getting some human WGS samples to complete after alignment to
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WGS segmentation fault
Hello, I'm having some issues getting some human WGS samples to complete after alignment to
4/18/17
Rajesh Patidar
,
Sean Davis
3
4/6/17
Missing a indel from targated sequencing
my maxInputDepth =10000 you can see whole config file here https://github.com/patidarr/ngs_pipeline/
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Missing a indel from targated sequencing
my maxInputDepth =10000 you can see whole config file here https://github.com/patidarr/ngs_pipeline/
4/6/17
Milan Domazet
,
B Bai
3
3/22/17
Q&A
A lot of calls when doing calling on a "dirty" sample
Hello Baoyan, sadly I did not find any issue for this. It would be good if we could get a hint from
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Q&A
A lot of calls when doing calling on a "dirty" sample
Hello Baoyan, sadly I did not find any issue for this. It would be good if we could get a hint from
3/22/17
Jason Walker
, …
napr
6
2/17/17
Exemplar alignment contains indel not found in the overlap indel set
Were you able to slove the error you mentioned? On Thursday, April 28, 2016 at 4:16:50 AM UTC-5,
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Exemplar alignment contains indel not found in the overlap indel set
Were you able to slove the error you mentioned? On Thursday, April 28, 2016 at 4:16:50 AM UTC-5,
2/17/17
napr
2/17/17
Error while using v1.0.15 on GSNAP aligned bam files
I am using strelka v1.0.15 on GSNAP aligned RNA-Seq data and i'm getting this error ERROR: Failed
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Error while using v1.0.15 on GSNAP aligned bam files
I am using strelka v1.0.15 on GSNAP aligned RNA-Seq data and i'm getting this error ERROR: Failed
2/17/17
Milan Domazet
1/30/17
Which Strelka to use?
Hello, I can see there is Strelka workflow and Strelka app standalone. It seems that workflow is
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Which Strelka to use?
Hello, I can see there is Strelka workflow and Strelka app standalone. It seems that workflow is
1/30/17
Lucas Lochovsky
1/26/17
ERROR: BAM headers and reference fasta disagree on chromosome: 'NC_007605'
Hi all. I've encountered this issue in Strelka where the input is a set of BAMs I've
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ERROR: BAM headers and reference fasta disagree on chromosome: 'NC_007605'
Hi all. I've encountered this issue in Strelka where the input is a set of BAMs I've
1/26/17