Entering edit mode
4.8 years ago
NT
▴
20
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