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mutSigCV "category discovery" in coverage files
Dear MutSig Expert,
Could someone explain to me what exactly the "category discovery" does when running mutSigCV? This is the step when you input a common coverage file (such as exome_full192.coverage.txt) and select genome build as hg19 or hg18.
I get confused because I thought that by using exome_full192.coverage.txt, the coverage file should be the same across different analysis, which is not what I observed in real data analysis. I analyzed the LUSC data as in the example file and my own data set, mutSig gives different coverage files, although they both starts with file exome_full192.coverage.txt.
Any explanation is welcome. Thanks a lot.