I am wondering whether MuSiC uses soft-clipped bases in its coverage and background mutation rate calculations.
I have generated somatic variant calls from WES tumor/normal pairs using MuTect2 with the --dontUseSoftClippedBases option, and I want to be sure that the coverage used for the bmr calculation matches the coverage that was actually used for calling variants. I'm not sure if I need to trim these bases out of the bam files before passing them to MuSiC, or if they would be ignored anyway.
Thank you for your help!
Best regards, Kate