MutSigCV Error List / Coverage file generation process

Good morning,

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)
MutSig_preprocess(mutation_file,coverage_file,covariate_file,output_filestem,varargin{:})"

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,

David

dw19@rice.edu

MutSigCV Error List / Coverage file generation process

"Error using MutSigCV>MutSig_preprocess (line 524)
probably build mismatch with chr_files

This error indicates that the base in the Reference_Allele column does not match the base in the genome reference.

2) The example coverage file for LUSC was based on the actual coverage, based on the BAM file using the WIG file as an intermediate step. It depends on Broad's capture bait set, which should be similar to what is used elsewhere. The general exome file is based on theoretical, uniform 100% coverage of the exome. Using real coverage information will give you better results.

Gordon

Hi Gordon, We are trying to

Hi Gordon,

We are trying to run Mutsig but are getting the "nonsilent and silent rates too different" error, which(after going through the code and analysing our input files) seems to be due to the coverage file being used. I have 2 questions regarding this:

1. We want to use our own coverage file, so can you please tell us the steps for generating it from bam/wig file.
2. If we comment that condition(line 826 in MutSigCV.run) and run Mutsig, will it make a lot of difference?