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GATK4 Mutect2 variant with a "germline" flag from unmatched tumors
Hi GATK team,
I have been calling somatic mutations from unmatched tumor samples using the latest GATK4 and found one of the well known EGFR exon deletion variants was flagged as "germline" (please see below) even though it is not present in the germline resource (af-only-gnomad.raw.sites.b37.vcf.gz). I was wondering how GERMQ is calculated.
7 55242465 . GGAATTAAGAGAAGCA G . germline CONTQ=93;DP=58;ECNT=1;GERMQ=1;MBQ=34,35;MFRL=188,206;MMQ=60,60;MPOS=34;POPAF=7.30;RCNTS=0,0;ROQ=93;SEQQ=93;STRANDQ=93;TLOD=70.40 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:36,20:0.362:56:22,13:11,7:21,15,12,8