I have downloaded all the VCF files for one cancer type from the TCGA. Upon annotation using Annovar, I notice that there are a lot more variants than I expected. So I have a few questions:
- How should I process these downstream? I've already reduced the list based on those that passed.
- I particularly wanted the mutation profiles of individuals before MutSig. Is using the VCF files the best way to do this, or should I just get the MAF file? My assumption was that the MAF file was MutSig processed.