1. In exploring the capabilities of MutSigCV, particularly in the instance where all that is available is a MAF file, I have encountered the error message below and would love to know what caused it. More generally, is there a list of errors thrown by the program and what their cause/resolution might be?
"Error using MutSigCV>MutSig_preprocess (line 524)
probably build mismatch with chr_files
Error in MutSigCV (line 184)
2. When utilizing MutSigCV on the LUSC data, I notice that the differences between significantly mutated genes as found by using the example data with coverage file found on this website and those found by using only the MAF file (and of course the general exome_full192.coverage.txt and hg19 files) are quite large. Is there a reference which might point to why this would be and your methodology in generating the coverage file specific to the LUSC cases?
Much thanks for you time,