Does MuTect work with MutSig?
Dealing with tumor samples, we have several that have matched normal, but not all. It seems to make sense to use MuTect for the samples with matched normal.
I noticed that MutSig uses .maf files for input. What is the best way to generate these input files? GATK indel realignment, calibration, haplotype caller, or?
Will MutSig accept files generated with MuTect, or are these mostly used independently?