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Disconcordant between VCF file and WIG in MuTect

JiantaoShiJiantaoShi BostonMember ✭✭
edited August 2014 in Ask the GATK team

As described the WIG contains the callable loci (14 reads in tumor sample and 8 reads in control sample). Then I compared called variants in VCF file to the callable loci in the WIG file, I found a high coverage locus called as somatic SNVs but listed as 0 in WIG file:

19 54726082 rs199959573 C T . MuTect DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0:22,0:.:18:0.00:0 0/1:28,3:34:31:0.097:2

So according the VCF file, the coverage in Tumor and Normal are 31 and 22. Is there a reason that this site are not callable by MuTect ?



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