Mutect2: NuMTs filtering on RNA-seq

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Leore Nehemie Bensabath

• January 29, 2021 15:57

Hi GATK Team, 

I am using Mutect2 in mitochondrial mode on rat RNA-seq data (I don't have WGS data available). 

It is not super clear to me if filtering NuMTs with the flag --autosomale-coverage of FilterMutectCalls also works with RNA-seq data, since the mtDNA has its own transcription initiation mechanism different from the nuclear one. Could you please help me with that ?  

Thanks ! 

Léore

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  Genevieve Brandt (she/her)

  • May 17, 2021 18:22

  Hi Leore Nehemie Bensabath,

  This should work, provided that you interpret autosomal coverage correctly. The autosomal coverage represents the average coverage of the autosome in the BAM. For RNA, it would represent how much autosomal RNA is in your BAM. So, the value might be different with RNA seq but it won't change your ability to use the flag.

  Best,

  Genevieve

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  Bhanu Gandham

  • January 29, 2021 19:46

  Hi ,

  The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

  Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

  We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

  For context, check out our support policy.

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