I was wondering if you would help in in the following: using Mutect, I have generated Wiggle coverage files for each of the matched tumor-normal pairs which I am analyzing. I was wondering the methodology/tool which the Broad uses to generate the gene/effect/categ table necessary for input into MutSigCV.
The documentation states: "This tab-delimited file can be produced by processing the sample-level coverage files in WIG (wiggle) format output by the MuTect tool." I'm wondering how best to go about doing so. Any insight would be much appreciated.