Hello community,

I am currently working on estimating tumour mutational burden using the RNA-Mutect-WMN pipeline. The process requires an output from RNA-Mutect, which in turn needs the output of Mutect2.

I have proceeded with the following steps:

1. Acquired tumour RNA-seq fastq files.
2. Executed Mutect2 in tumour-only mode to generate a VCF file.
3. Performed filtering on the VCF and subsequently annotated it using Funcotator (a successor to Oncotator), resulting in MAF files
4. Used the aforementioned MAF file for RNA-Mutect

The initial steps with RNA-Mutect run smoothly, but I encounter issues during the filtering step where MATLAB files come into play. I receive errors related to mismatched column names, and the row numbers do not align as expected. I attempted using other annotators such as VEP and Annovar, but they do not yield the required columns for compatibility.

A specific challenge is the FilterRNAMutationsNoPoN binary executable; since the source script isn't available, troubleshooting is proving to be difficult.

Could anyone provide insights or suggestions on how to resolve these discrepancies and proceed with the workflow? I would greatly appreciate any guidance.

Thank you!