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[GATK 4 beta] clustered_events in Mutect2/FilterMutectCalls
I have a question about filtering Mutect2 calls. A well-characterized SNV (vcf records below 17:7577120) is filtered out by clustered_events filter. It appears that an artificial haplotype is assembled to have the SNV along with other variations nearby. But those variations don't appear in the same read and it seems unlikely to me that those coexist in one haplotype, so I am hesitant to configure a higher value for --maxEventsInHaplotype.
Do you think it is reasonable? If so, I wonder how I can get the variant (17:7577120) not-filtered (and variants on the left filtered).
17 7577079 . CTTCCT C . clustered_events DP=592;ECNT=5;NLOD=95.58;N_ART_LOD=-2.510e+00;POP_AF=1.000e-03;P_GERMLINE=-9.228e+01;TLOD=18.63 GT:AD:AF:MBQ:MCL:MFRL:MMQ:MPOS:OBAM:OBAMRC:PGT:PID:SA_MAP_AF:SA_POST_PROB 0/0:316,0:0.019:41,0:0,0:413,0:60,0:41,0:false:false:0|1:7577079_CTTCCT_C 0/1:265,8:0.042:41,41:0,0:410,416:60,60:37,59:false:false:0|1:7577079_CTTCCT_C:0.030,0.020,0.029:4.069e-03,3.816e-03,0.992 17 7577087 . GT G . clipping;clustered_events;read_position DP=570;ECNT=5;NLOD=93.62;N_ART_LOD=-2.494e+00;POP_AF=1.000e-03;P_GERMLINE=-9.031e+01;TLOD=18.71 GT:AD:AF:MBQ:MCL:MFRL:MMQ:MPOS:OBAM:OBAMRC:PGT:PID:SA_MAP_AF:SA_POST_PROB 0/0:302,0:3.807e-05:41,0:0,0:416,0:60,0:40,0:false:false:0|1:7577079_CTTCCT_C 0/1:260,8:0.029:41,0:0,0:416,416:60,60:40,0:false:false:0|1:7577079_CTTCCT_C:0.030,0.020,0.030:4.483e-03,3.633e-03,0.992 17 7577089 . G A . clipping;clustered_events;read_position DP=566;ECNT=5;NLOD=91.51;N_ART_LOD=-2.484e+00;POP_AF=1.000e-03;P_GERMLINE=-8.821e+01;TLOD=18.76 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:MBQ:MCL:MFRL:MMQ:MPOS:OBAM:OBAMRC:OBF:OBP:OBQ:OBQRC:PGT:PID:REF_F1R2:REF_F2R1:SA_MAP_AF:SA_POST_PROB 0/0:297,0:3.822e-05:0:0:NaN:41,0:0,0:413,0:60,0:40,0:false:false:.:.:.:.:0|1:7577079_CTTCCT_C:154:143 0/1:261,8:0.030:2:6:0.250:41,0:0,0:418,416:60,60:39,0:false:true:0.750:0.038:44.92:100.00:0|1:7577079_CTTCCT_C:133:128:0.030,0.020,0.030:4.595e-03,3.543e-03,0.992 17 7577090 . CGCCGGT C . clipping;clustered_events;read_position DP=579;ECNT=5;NLOD=93.27;N_ART_LOD=-2.494e+00;POP_AF=1.000e-03;P_GERMLINE=-8.997e+01;TLOD=18.63 GT:AD:AF:MBQ:MCL:MFRL:MMQ:MPOS:OBAM:OBAMRC:PGT:PID:SA_MAP_AF:SA_POST_PROB 0/0:305,0:4.990e-03:41,0:0,0:416,0:60,0:40,0:false:false:0|1:7577079_CTTCCT_C 0/1:266,8:0.030:41,0:0,0:417,416:60,60:39,0:false:false:0|1:7577079_CTTCCT_C:0.030,0.020,0.029:4.692e-03,3.389e-03,0.992 17 7577120 . C G . clustered_events DP=520;ECNT=5;NLOD=82.01;N_ART_LOD=-2.443e+00;POP_AF=2.462e-05;P_GERMLINE=-8.032e+01;TLOD=188.97 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:MBQ:MCL:MFRL:MMQ:MPOS:OBAM:OBAMRC:OBQ:OBQRC:REF_F1R2:REF_F2R1:SA_MAP_AF:SA_POST_PROB 0/0:273,0:0.016:0:0:NaN:41,0:0,0:415,0:60,0:39,0:false:false:.:.:135:138 0/1:191,56:0.233:26:30:0.536:41,41:0,0:418,388:60,60:37,44:false:false:54.12:100.00:102:89:0.222,0.202,0.227:9.482e-03,0.012,0.978