I am calling somatic variants using Mutect2 in paired mode. After variant calling, I applied FilterMutectCalls, followed by annotation using Funcotator. I wanted to ask whether there are any additional GATK steps or commands recommended for hard-filtering beyond this workflow. I have performed all these steps using the latest version of GATK (v4.6.2.0).
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written
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sk_24 •
1 answer
Filtering somatic variants is sort of a "dark art" where you will have dive through lots references and manuals. Though it is never clear wether these still apply.
The Cancer Genome in a Bottle Project:
has published a number of workflows (though a bit hard to locate on the site).
I would consider these workflows and filtering steps the "latest and best" recommendations.
If you Google for these filtering you will get lots of hits to NextFlow or Snakemake prebuilt workflows, I even found one published by NVIDIA:
https://docs.nvidia.com/clara/latest/tutorials/how-tos/somaticcalling.html
reading this latter, I chuckle how in the era of LLMs and highly intelligent AI Agents one of the sophisticated steps described is grepping and running awk ...
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Did you read through GATK Best Practices?