Hello, I am currently building an analysis workflow using Parabricks.
I previously used Mutect2 on a CPU machine for mitochondrial variant detection, and I would like to use it in GPU Parabricks as well.
However, I couldn’t find any mention of the Mitochondrial mode on the mutectcaller documentation page, and I am unsure how to configure it.
How can I replicate the parameter settings that are automatically applied in Mutect2’s Mitochondrial mode for mutectcaller?
Regards.
Hi @yskishr,
We do not currently support mitochondrial mode in Parabricks.
To dig a little deeper, according to GATK “[the --mitochondrial flag] sets --initial-tumor-lod to 0, --tumor-lod-to-emit to 0, --af-of-alleles-not-in-resource to 4e-3, and the advanced parameter --pruning-lod-threshold to -4”. The only flag that is not supported in Parabricks right now is --af-of-alleles-not-in-resource to 4e-3 but without that, we don’t fully support mitochondrial mode.
Thank you for your prompt reply.
I understand that Mutectcaller does not have a Mitochondrial mode.
In that case, is there any Parabricks tool that can detect mitochondrial variants other than Mutectcaller?
No problem! As far as I know, there are not other ways to detect mitochondrial variants using Parabricks.
Thank you for the clarification.
I will proceed with running the mt variant detection on CPU.
Thank you very much.