Hello! I am using GATK4 MUTECT2 for calling somatic variants from the whole genome sequencing dataset. I have noticed that MUTECT2 have a ‘mitochondria mode’ (https://gatk.broadinstitute.org/hc/en-us/articles/360042477952-Mutect2). However, from the documentation it seems that all variants (i.e. germline and somatic) in mitochondria will be detected using MUTECT2, instead of only somatic variants. May I know if my understanding is right? If yes, is there a tool that could be used to call only somatic variants in mitochondria? Any suggestion is appreciated. Thanks!
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