Hi,

I am a newbie. I do not have mutect files but I have few .maf files (one maf file per cancer type), downloaded from TCGA. Is it possible to work with these .maf files on SomaticSignatures? I appreciate for your help.

You can use the functions in the SomaticCancerAlterations package to import MAF files, see my answer in Package SomaticCancerAlterations, import own .maf file?. Please note that MAF files are not very well defined, and different pipeline have different ways of formatting them. If possible, try to get your data in a more standardized format, such as VCF - but I know that this can get tricky with TCGA data.