Mutect2's support for MNP in GATK 4.1.8.1?

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Bing

• July 23, 2020 01:29

Can you please provide
a) GATK version used: 4.1.8.1
b) Exact GATK commands used: None
c) The entire error log if applicable: None

 

Dear staff,

We know that, in previous versions of GATK, like 4.1.2, Mutect2 does not support MNPs, and should add an argument of "--max-mnp-distance 0" to inhibit MNPs.

 

I noticed that in the relase information of 4.1.8.1, it is announced that MNPs are supported.

Should we remove "--max-mnp-distance 0" in Panel of Normals creating and Mutation Calling?

 

Thanks

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  Genevieve Brandt (she/her)

  • July 23, 2020 16:01

  Hi Bing, I don't see any information in our release notes about supporting MNPs: https://github.com/broadinstitute/gatk/releases. From the update with 4.1.6.0, it looks like there was a bug with --max-mnp-distance 0 not performing correctly and causing issues with GenomicsDBImport, and now the option works correctly. 

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  David Benjamin

  • July 24, 2020 03:31

  @Bing It's worth clarifying that Mutect2 and FilterMutectCalls themselves have not had problems with MNPs and that -max-mnp-distance has worked as intended.  The issue is in the GenomicsDBImport tool, which is part of our panel of normals creation workflow.  If you want to call MNPs you can generate a panel of normals using -max-mnp-distance 0 but then run Mutect2 with a non-zero value.  The panel will still work and you will get MNP calls.

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  Bing

  • July 24, 2020 03:53

  @Genevieve Brandt  @David Benjamin

  You've made things clear. Thank you very much!

   

   

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