Hi, we have been using GATK v184.108.40.206 for paired tumor/normal analysis and noticed a discrepancy in the way Mutect2 is calling the REF/ALT alleles at one of the sites. I've attached an IGV screenshot showing the original tumor BAM file used as input to Mutect2 (on the top) and the assembled haplotypes containing BAM output file written by Mutect2 using -bamout option (at the bottom). Both the BAM files point to the same change: GTT > AA. The top one represents it as a deletion of G followed by 2 SNVs, while the bottom one represents it as a deletion of GTT followed by an insertion of AA.
While Mutect2 is haplotyping this event correctly as evidenced in the output BAM, the variant call reported in the VCF file looks incorrect. It's reporting it as a deletion of GTT, and has skipped the insertion of AA. Any idea why this is happening and how to resolve the same? Thanks!
13 32953885 . AGTT A . . DP=230;ECNT=1;MBQ=34,35;MFRL=199,220;MMQ=60,60;MPOS=22;NALOD=1.94;NLOD=24.03;POPAF=6.00;TLOD=182.86 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:86,49:0.381:135:49,24:33,24:64,22,35,14 0/0:90,0:0.011:90:45,0:42,0:68,22,0,0
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