I am trying to used MutSigCV to analyze my own WES data. Several input files were required, including MAF file, one coverage file and one covariate file. Although the document provided one alternative
all-purpose coverage file, I think a coverage file created from my own data may generate more accurate results. The document pointed out that this tab-delimited coverage file can be produced by processing the sample-level coverage files in WIG (wiggle) format output by the MuTect tool. But no more details, could you provide more details about how to create specific coverage file. A example will be the best. Hope your response! Appreciate! Best wishes for you during worldwide pandemic.
The follwoing is buid-in coverage file in the example file of the software(LUSC.coverage.txt), this is what I want to create.