Calling somatic mutations with RNA-seq data

[hukai916]

Hi there,

Just wondering if there is a best-practice pipeline for calling somatic mutations using RNA-seq data. I noticed a discussion here: https://gatk.broadinstitute.org/hc/en-us/community/posts/23387556065691-Somatic-and-germline-mutations-from-RNA-seq-data and it says that HaplotyeCaller assumes a germline model, does it mean that HaplotypCaller will not capture any somatic mutations at all?

I am aware that Mutect2 can detect somatic mutation but it requires DNA-seq data. Is it possible to repurpose it to take RNA-seq data for somatic mutation calling, any caveats? Any input will be highly appreciated!

Thanks,

--Kai