Hi everyone
I have been trying to run RNA_MUTECT_1.0_1 for a while now. A lot of tools used by the pipeline are older versions and are now replaced by newer tools. Oncotator --> funcotator Mutect --> Mutect2
I am mainly struggling with the output of Mutect2, which is not compatible with the Matlab scripts. I am now trying to convert this output to the output of Mutect; making it compatible for the Matlab scripts. This is however not very easy.
Furthermore, I want to use this output for https://github.com/yizhak-lab-ccg/RNA_MUTECt_WMN. However, other issues arise with this pipeline. It requires an RNA PON from GTEx, which is not findable anymore. (we have access)
Does anyone have any insight on this, or has tried this before? Any help would be greatly appreciated!
Kind regards Charlotte
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Charlotte Stubbe •
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Hi, Charlotte. Thanks for reaching out.
Can you please help provide the following?
What does your current output look like? Do you have a minimum reproducible example of your code? What errors are you running into? Which version of GATK/Mutect2 are you using?
In general, it can be tricky to modify the native output formats from tools like Mutect2 because downstream scripts often expect very specific fields. Sometimes it’s easier to adapt the parsing script rather than transforming the variant caller output itself, but it would help to see the exact mismatch you’re encountering.
Happy to take a look if you can share an example.