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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