I'm a beginer with MutSigCV, I had ran it with example files successfully.But I really don't konw how to produce the maf,coverage and covariates table from raw sequencing data,which I have 40 CRC whole-genome(cancer-normal),that want to detect mutation significant genes.Which software should I use step by step? and the pipeline to use MutSigCV?
You don't really need coverage and covariates table (mutsig comes with some of these files, in case you don't have). But maf file is necessary. Read about maf specification here.
For mutsig, 9 fields are necessary.
Hugo_Symbol, Chromosome, Start_Position, End_Position, Reference_Allele, Tumor_Seq_Allele1, Tumor_Seq_Allele2, Variant_Classification, Tumor_Sample_Barcode
You can use this script to generate maf file.