BisSNP generate empty output file

[Divya Srivastava]

Hello

I am using BisSNP-0.82.2 but it generate an empty output files of cpg.vcf and snp.vcf

Command used:
java -Xmx4g -jar BisSNP-0.82.2.jar -R /home/genomics2/tools/For_METHGO/ALM_BS_genome_new.fasta -T BisulfiteGenotyper -I /home/genomics2/tools/For_METHGO/ALM1Fd_R1_paired_trimmed_withRG.bam -D /home/genomics2/tools/For_METHGO/dbSNP/merge_new_dbSNP21.vcf -vfn1 /home/genomics2/tools/For_METHGO/dbSNP/cpg1.raw.vcf -vfn2 /home/genomics2/tools/For_METHGO/dbSNP/snp1.raw.vcf -L /home/genomics2/tools/For_METHGO/ALM1_R1_paired_vcf_lenght.bed

Is there any suggestion how I sort this error, I also attach all the output files with this post.

Thanks in advance.

[ping]

Dear Divya,

I was out of town and sorry for the late reply. There are several possibilites:

1. inconsistent "chr" usage in bam file and your ALM1_R1_paired_vcf_lenght.bed file. One with chr, the other file without chr

2. could you add "-stand_call_conf 30 -stand_emit_conf 0" to see if there is still no output?

3. could you give me some part of your bam file? e.g. first 1000 rows. it could be due to some reason all of the reads are filtered out..

thanks,

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

[Divya Srivastava]

Thank you so much sir for your valuable reply ,

It's very useful for my analysis and finally I get snp.vcf file after adding "-stand_call_conf 30 -stand_emit_conf 0" in my command line.

But can you please explain me on which basis you set the value of -stand_call_conf is 30 because the default value is 20 and stand_emit_conf  is 0. I am confuse.

Please explain me if possible.

Thanks, 

Divya.

[Lyping1986]

Hi Divya,

Sorry for my mistake. 20 should be the parameters, not 30

Yaping

Sent from my iPhone

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