HI I am using the mutsig to analyze my data. I not that mutsig has an preprocess step to calculate the categ column from the MAF input file. This step requires a genome reference file for its inference. However, though I include the genome build files in my input as below: MutSigCV('F:LUSC.MutSigCV.input.data.v1.0\LUSC.maf', 'F:exome_full192.coverage.txt', 'F:LUSC.MutSigCV.input.data.v1.0\gene.covariates.txt', 'F:LUSC.MutSigCV.input.data.v1.0\output.txt', 'F:mutation_type_dictionary_file.txt', 'F:chr_files_hg19') the MutSig program still tells me: NOTE: unable to perform category discovery, because no chr_files available.Will use two categories: missense and null+indel
All of the files are download from the http://archive.broadinstitute.org/cancer/cga/mutsig_run. Could anyone who is expert in Mutsig gives me some help? Thanks
