How do I call somatic mitochondrial variants?

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Ruiqiao Bai

• September 14, 2021 04:03

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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  Genevieve Brandt (she/her)

  • September 14, 2021 16:21

  Hi Ruiqiao Bai,

  I am going to move your post into our Community Discussions -> Documentation Questions topic, as the Somatic topic is for reporting bugs and issues with GATK.

  You can read more about our forum guidelines and the topics here: Forum Guidelines.

  Best,

  Genevieve

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  Pamela Bretscher

  • September 20, 2021 17:05

  Hi Ruiqiao Bai,

  We do not currently have a pipeline specifically for somatic mitochondrial variants so the Mutect2 "mitochondrial mode" will most likely call some germline variants in addition to somatic variants. You can however try to run Mutect2 using a matched normal sample which may filter out a lot of the germline variants, though this is not something that has been tested in mitochondrial mode. I hope this is helpful and please let me know if you have additional questions.

  Kind regards,

  Pamela

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  Ruiqiao Bai

  • September 21, 2021 05:00

  Dear Pamela,

   

  Thanks a lot for your answer!

   

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