Re: BisSNP

[Yaping Liu]

Hi Alain,

Sorry for the late reply,m I have just come back from a vocation.

I will change vcf2bed.pl little late, which makes not convenient now…

 i think the problem here is that you have not specified "-stand_emit_conf", by default, "-stand_emit_conf " is 30, so when you specify -stand_call_conf 1, it takes not effect, because it is less than the emit threshold. please just add an option that "-stand_emit_conf 0"

Thanks,

Yaping Liu

PhD candidate 

in

USC Epigenome Center

University of Southern California

lypin...@gmail.com

On Oct 20, 2012, at 7:23 PM, Alain Pacis wrote:

Dear Yaping Liu,

My name is Alain Pacis and I am Master's student in bioinformatics at University of Montreal with Dr. Barreiro.
I am currently working on the dendritic cell (DC) methylome to find changes in DNA methylation before and after infection to Myobacterium tuberculosis (MTB).

I started using BisSNP to get both the SNPs and methylation data from my bisulfite-treated sample aligned using Bismark (~10X coverage).

The problem is that the FILTER column for both snp.raw.vcf and cpg.raw.vcf output files doesn't indicate "PASS" and therefore vcf2bed.pl won't work unless that column indicates "PASS".

I even put the parameter stand_call_conf = 1 but it still did not work.

I used the following command:

java -Xmx48g -jar /RQusagers/pacisala/barreiro_group/ALAIN/BisSNP/BisSNP-0.73.jar -R /RQusagers/pacisala/barreiro_group/ALAIN/BisSNP/hg19_rCRSchrm.fa -T BisulfiteGenotyper -nt 12 -stand_call_conf 1 -I NEG81.adapt.fastq_bismark.sam_deduplicated.header.sorted.realigned.recal.bam -D /RQusagers/pacisala/barreiro_group/ALAIN/BisSNP/dbsnp_135.hg19.sort.sorted.again.vcf -vfn1 cpg.raw.vcf -vfn2 snp.raw.vcf

Thank you.

--
Alain Pacis

[Raphaël Poujol]

HAHA ! Hi Alain (I had to comment the line 47 to make it run)

So you are using BisSNP now ?

[Yaping Liu]

Where did you download vcf2bed.pl from SVN repository or website?

I just wondering if i forgot to update the newest version perl script.

Yes, the center is using it right now. But we have several different version for different purpose..

yaping

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[Raphaël Poujol]

Hi Yaping !

It s because I don t have PASS in any of my vcf as you notice in an other thread.
I am trying to recalibrate my alinment file in case missing this step was important.
How do you explain that PASS is totally absent of my data ?

thanks

Raphael

[Raphaël Poujol]

Sorry, it s -stand_emit_conf 0 !

[Yaping Liu]

Exactly!

[Barbara Zambiasi Martinelli]

Hi all,

So should I just comment the line 47 of vcf2bed.pl ? I did it and it is working, but I want to make sure that this is the solution for the problem in the script, returning a reliable result.

Thanks in advance,

Barbara

[ping]

Hi Barbara,

Yes. If you want to export all of the location in your vcf file.

yaping

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Yaping Liu, Ph.D.

Postdoctoral Associate

Manolis Kellis Lab

Computer Science and Artificial Intelligence Lab (CSAIL)
Massachusetts Institute of Technology

Broad Institute of MIT and Harvard

Office Phone: +1 617 324 8436 
Email: 

lypin...@gmail.com

yap...@mit.edu

lyp...@broadinstitute.org

[Barbara Zambiasi Martinelli]

Yes, this is the case. Thank you very much, Yaping.

Barbara

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