Hi,
I've been calling somatic mutations with Mutect2, and have noted that the AF calculation does not always correlate to DP alt/(DP ref+DP alt). For example, consider this indel:
T057.mutect2.vcf:7 17379247 . CAACAGCAACAGTCCTTGGCTCTGAACTCAAGCTGTATGGTACAGGAACACCTACATCTAG C . PASS ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=57.68;TLOD=106.87 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:66,30:0.452:18:12:.:1983,919:32:34 0/0:214,0:0.112:0:0:.:6285,0:98:116
The tumour variant AF should be (30/(30+66)=0.31, but is reported as 0.42, while the normal variant AF should be 0/214=0, but is reported as 0.112
Am I missing something/misinterpreting these fields?
Any comments and help greatly appreciated!
Thanks,
Stephen
