Hi,

I'm using mutect2 with a panel of normal. However, i have an issue with filtermutectcalls step. It filters real somatic mutations like R132C for IDH1 and R172G for IDH2 as clustered_events and mutliallelic sites. I didn't change any parameters of mutect2 or filtermutectcalls. Also there is no variants of these two positions in the panel of normal that i have constructed. what can I do so that these two mutations and maybe, other real somatic mutations will not be filtered as clustered_events or multiallelic sites

Thank you

grep '209113113'  *_filtered.vcf
_filtered.vcf:chr2        209113113       .       G       A       .       clustered_events        CONTQ=93;DP=1404;ECNT=3;GERMQ=93;MBQ=27,34;MFRL=176,183;MMQ=60,60;MPOS=19;POPAF=7.30;SEQQ=93;STRANDQ=93;TLOD=1468.44      GT:AD:AF:DP:F1R2:F2R1:SB        0/1:853,502:0.371:1355:424,241:388,244:400,453,251,251

grep '90631839'  *_filtered.vcf
_filtered.vcf:chr15       90631839        .       T       C,TCACCATTGGCGGGCAC     .       clustered_events;multiallelic   CONTQ=93;DP=3003;ECNT=9;GERMQ=56;MBQ=29,28,29;MFRL=140,151,130;MMQ=60,60,60;MPOS=19,0;POPAF=7.30,7.30;SEQQ=93;STRANDQ=93;TLOD=3385.74,31.10       GT:AD:AF:DP:F1R2:F2R1:SB        0/1/2:1523,1288,23:0.457,8.221e-03:2834:752,619,16:725,629,1:754,769,685,626