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Over estimation of AF in Mutect2 (GATK 18.104.22.168) ?
I ran Mutect2 (GATK 22.214.171.124) followed by FilterMutectCalls with default parameters. I got some passed variants with AF much larger than the alt_depth/total_depth (see attached image), I checked the reads mapping qualities and most of them are good, so reads are not likely filtered by Mutect2.
Why is the AF larger than the alt_depth/total_depth?
I noted that the three variants with AF overestimated also with reads orientation bias, can Mutect2 filter variants by reads orientation bias?
chrX 41000336 . A G . PASS DP=2025;ECNT=1;NLOD=241.68;N_ART_LOD=-6.740e-01;POP_AF=1.000e-03;P_GERMLINE=-2.387e+02;TLOD=5.88 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:OBAM:OBAMRC:OBF:OBP:OBQ:OBQRC:SA_MAP_AF:SA_POST_PROB 0/1:1094,7:0.030:563,1:531,6:33:200,195:60:33:false:false:.:.:100.00:51.51:0.010,0.010,6.358e-03:6.461e-04,1.733e-03,0.998 0/0:828,2:0.028:422,1:406,1:34:199,181:60:19:false:false
chrX 66766308 . A G . PASS DP=1691;ECNT=2;NLOD=90.81;N_ART_LOD=-1.323e+00;POP_AF=1.000e-03;P_GERMLINE=-8.780e+01;TLOD=6.03 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:OBAM:OBAMRC:OBF:OBP:OBQ:OBQRC:SA_MAP_AF:SA_POST_PROB 0/1:1292,8:0.029:578,0:714,8:32:291,291:60:38:false:false:.:.:100.00:51.51:0.010,0.00,6.154e-03:7.151e-04,2.907e-03,0.996 0/0:314,1:0.033:152,0:162,1:32:191,297:60:15:false:false
chrX 66766320 . C T . PASS DP=1382;ECNT=2;NLOD=74.68;N_ART_LOD=-2.139e+00;POP_AF=1.000e-03;P_GERMLINE=-7.140e+01;TLOD=7.39 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:OBAM:OBAMRC:OBF:OBP:OBQ:OBQRC:SA_MAP_AF:SA_POST_PROB 0/1:1060,10:0.030:453,0:607,10:30:292,329:60:32:false:false:.:.:100.00:52.34:0.010,0.010,9.346e-03:0.042,4.118e-04,0.957 0/0:256,1:0.029:124,0:132,1:20:186,135:60:32:false:false