Inferring tumor mutational burden from RNA-seq data

Question

[Aaron]

Hi all, I recently found a package called RNA-MUTECT-WMN for estimating tumor mutational burden from RNA-seq data that I have been eager to use, but I’ve had some trouble figuring out how to run a prerequisite for using the WMN package, called RNA-MUTECT_1.0-1. The data I have was generated from GRCm38 (mm10). I have never used .maf files before, but I’ve seen .maf files generated for individual chromosomes as opposed to a whole genome, and have been led to believe that they should be submitted to the RNA-MUTECT_1.0-1 scripts individually - is this right? If so, which RNA-MUTECT_1.0-1 shell script should I use if my end goal is to use RNA-MUTECT-WMN? Would you happen to have a real example script?