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"PASS" somatic variant has no supporting reads #12

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likelet opened this Issue Aug 3, 2017 · 5 comments

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likelet commented Aug 3, 2017

Hi
here is the output by strelka somatic calling mode
chr16 50327364 . C T . PASS SOMATIC;QSS=53;TQSS=1;NT=ref;QSS_NT=53;TQSS_NT=1;SGT=CC->CC;DP=52;MQ=60.00;MQ0=0;ReadPosRankSum=0.00;SNVSB=0.00;SomaticEVS=20.72 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 51:0:0:0:0,0:47,48:0,0:4,4 0:0:0:0:0,0:0,0:0,0:0,0
The last field corresponds the reads count information in tumor samples. However, there's no reads at all but it is marked as "PASS" somatic snv.
how dose this happen?
my strelka version is strelka-2.7.1.centos5_x86_64.

thanks!

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ctsa commented Aug 3, 2017

This is unexpected. When you view the tumor locus is there any sequencing coverage?

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likelet commented Aug 4, 2017

hi ctsa, thanks for your quick response. Actually, i have viewed the reads distribution using IGV, and comfirmed that the reads coverage info presented in vcf was corrected. So i think this may be caused by other possible reseasons involved in somatic calling algorithm.

To cope with this, i just added an extra filtering step in term of minimum reads number supporting alterations.
any suggestions for that ?

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ctsa commented Aug 4, 2017

If you can share (or privately share) the IGV screenshot or a bam snippet covering the locus we can try to cover this. I haven't seen this pattern before so it's difficult to suggest what would help.

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likelet commented Aug 4, 2017

Well, here is the IVG screenshot
igv_screenshot

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ctsa commented Aug 4, 2017

Thank you. Will try to reproduce.

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