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Is normal-artifact-lod too stringent in FilterMutectCalls
FilterMutectCalls from gatk 22.214.171.124, I see that the
--normal-artifact-lod option is set to 0.0 and I wonder whether this is too stringent.
The variant below has been flagged as
artifact_in_normal for having N_ART_LOD=0.953 which results from 1 mismatching read out of 45 total reads (I checked the alignments and there are no other mismatching reads). Considering that the tumour has loads of supporting reads (REF, ALT: 44, 42) this variant would be rejected despite being a likely true positive.
Maybe one should also consider the difference between N_ART_LOD and/or TLOD and/or NLOD?
chr12 25245351 . C A . artifact_in_normal DP=135;ECNT=1;NLOD=9.27;N_ART_LOD=0.953;POP_AF=1e-05;P_CONTAM=0;P_GERMLINE=-7.979;TLOD=149.47;CSQ=A|...|HGNC:6407| GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:44,42:0.49:11,13:33,29:38:167,154:60:15:0.444,0.475,0.488:0.038,0.012,0.949 0/0:44,1:0.043:12,0:32,1:38:169,135:60:20:.:.
Any thoughts much appreciated!