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How does Mutect2 deal with SoftClip bases?
Hi , I get a variant record like this using GATK188.8.131.52 Mutect2 tumoronly mode.
It seems that the insertion is caused by softclip bases. Please see the IGV snapshot( I have turned on "Show soft-clipped bases").
chr16 68845762 . G GAGTTTCCCTACGTATACCCTGGTGGTTCAAGCTGCTGACCTTCAAGGT . read_position CONTQ=35;DP=40;ECNT=1;GERMQ=84;MBQ=37,40;MFRL=257,1656;MMQ=60,60;MPOS=0;POPAF=7.30;SAAF=0.00,0.071,0.075;SAPP=0.180,3.791e-03,0.816;TLOD=7.89 GT:AD:AF:DP:F1R2:F2R1:OBAM:OBAMRC 0/1:37,3:0.095:40:24,0:13,3:false:false
I want to know how Mutect2 deals with soft-clipped bases? And how Mutect2 flags the "read_position" filter tag.