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uclahs-cds / pipeline-call-sSNV

A Nextflow pipeline to identify the somatic single nucleotide variants (sSNVs) by comparing a pair of tumor/normal samples.
https://uclahs-cds.github.io/pipeline-call-sSNV/
GNU General Public License v2.0
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consider adding mitochondrial mode for Mutect2 #144

Open sorelfitzgibbon opened 1 year ago

sorelfitzgibbon commented 1 year ago

Mutect2 has a mitochondrial mode that deals with issues specific to mitochondrial variant calling, discussed here: https://github.com/broadinstitute/gatk-docs/blob/master/blog-2012-to-2019/2019-03-05-New!_Mitochondrial_Analysis_with_Mutect2.md

maotian06 commented 1 year ago

This is interesting! I was wondering about the accuracy compared to call-mtSNV!

sorelfitzgibbon commented 1 year ago

Currently the pipeline is using normal Mutect2 on chrM. Should chrM either be removed from the calling, or should call-mtSNV be pulled in to make the calls?

yashpatel6 commented 1 year ago

Just a quick thought, if we were to add Mutect2 mitochondrial calling, we'd want to add it to call-mtSNV since we have a pipeline set up for that specific purpose. I'm not sure whether we want to remove it here or keep it as is and advise users to use call-mtSNV calls for mitochondrial variants.

tyamaguchi-ucla commented 1 year ago

Just a quick thought, if we were to add Mutect2 mitochondrial calling, we'd want to add it to call-mtSNV since we have a pipeline set up for that specific purpose. I'm not sure whether we want to remove it here or keep it as is and advise users to use call-mtSNV calls for mitochondrial variants.

Yup, that makes sense. Also, this task is considered low priority for now.