no somatic calls in output file

[Arshi Arora]

Hi,

I am running Strelka on a panel normal-tumor pair bam. I have set the isSkipDepthFilters = 1. But, I don't see any calls in the output results folder in the files - 

 wc -l *

  121 all.somatic.indels.vcf

  114 all.somatic.snvs.vcf

  121 passed.somatic.indels.vcf

  114 passed.somatic.snvs.vcf

The lines you see here is just the header information summarizing chr and VCF columns. 

I did run mutect on this pair also, and see about 12 mutations excluding GL chr etc. I am really interested in the indel calls from Strelka. 

Appreciate any help!

Thanks,

Arshi

[Tyler Funnell]

I have the same problem. Another tool produces thousands of mutations. I've tried isSkipDepthFilters=1 as well with no difference. This is only happening to 2 of my pairs though.

[Tyler Funnell]

In my case, it turned out to be an issue with the bams. Converting bam -> sam -> bam fixed the issue for me. The odd thing is that Strelka doesn't seem to notice a problem with those bams and produces no mutation calls. Other tools have no problem with them, but samtools tview complains (which is how I diagnosed the problem).

[Arshi Arora]

Thanks for posting here Tyler! I agree, in my case too something is wrong with the bam. But I do see calls from other tools.