Issues with FilterRNAMutationsNoPoN in RNA-Mutect Workflow for Tumour Mutational Burden Estimation
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:
- Acquired tumour RNA-seq fastq files.
- Executed Mutect2 in tumour-only mode to generate a VCF file.
- Performed filtering on the VCF and subsequently annotated it using Funcotator (a successor to Oncotator), resulting in MAF files
- 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!
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Hi khushi ahuja
This workflow is not part of our published workflows so our support will be very limited. Looks like the original workflow is tied to GATK version 4.2.6.1 and Funcotator resource for that version. From one version to another we have changes in the resource files and Funcotator functionality that may be causing the differences in the output. Our recommendation would be to follow the workflow as the author suggested and try to obtain resource file for GATK Funcotator 4.2.6.1. We may not provide additional support for the rest since the workflow is neither published nor endorsed by us.
Regards.
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