Does Genome MuSiC use soft-clipped bases in its coverage calculation?

Question

[kmegq]

Hello,

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

Answer 1

[Chris Miller]

I believe that the answer is no, as it's using the samtools libraries, and those do not return soft-clipped bases by default, IIRC. That said, it'd be easy to verify. Extract a dozen reads from a region of your bam file, choose a position that has both soft-clipped and non-soft-clipped bases, then run the tool just on that bam and that site. Also, the calcRoiCovg code is here, if it helps: https://github.com/ding-lab/calc-roi-covg/blob/master/calcRoiCovg.c