We've been working to create the correct files for MutSigCV and have run into a few problems. Hopefully these are solvable questions, and thank you for your time.
First, we are trying to create the coverage file for our sequencing, but in the mean time have been using the provided 'full exome coverage' file. If our data is whole genome, will this reference file be useful, being that it is labeled 'exome?'
Second, I have seen in some posts and threads that MutSigCV was to be incorporated into GenePattern; I haven't been able to locate it there, but it looks like in the "what's new" of the Firehose workflow, MutSig is there. Are there plans to incorporate it into GenePattern still?