In the sample file for MutSigCV gene coverage file, for each mutation, there is coverage for each sample.
Is this coverage the alternative coverage on tumor sample?
But if I try to get the information from MuTect2 output, I have the coverage only for tumor samples with mutation. Should I give 0 for all tumors without mutation on this location? I thought this is reasonable, but if I look at the sample data, all samples have non-zero value on all mutations.
I know we can just use the default file that MutSigCV provides, but I thought I could get more accurate results if I provide with more informative coverage file.