Mutect for Somatic SNVs in Highly Polymorphic Genome Regions

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Dario

• August 03, 2021 03:00

Could there be a document created which carefully explains somatic SNV calling in regions where the reference genome sequence is not representative of what most people have? There is the clunky PolySolver solution which depends on Docker and has minimalist end-user documentation. Could there be a solution built into GATK itself?

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  Genevieve Brandt (she/her)

  • August 03, 2021 22:42

  Thank you for posting your feature request Dario! If other users would find this feature useful, please interact with this post so we know if this is a popular request. I will follow up with our developer team to make sure that they hear this request and can work on it when their schedule allows.

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  ਅਮਰਿੰਦਰ | Amarinder

  • August 07, 2021 04:25

  Thanks, Dario, for posting this. Genevieve Brandt (she/her) I also think, this is required especially for genomic regions Such as HLA and will be useful for many users working on it. 

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  Genevieve Brandt (she/her)

  • October 26, 2021 21:31

  Hi ਅਮਰਿੰਦਰ | Amarinder and Dario,

  Right now this is not something we are able to support.

  I brought this up with our Mutect2 developer and he suggested grabbing reads from the HLA contigs of the matched normal,  de novo assembling those reads, and using that assembly as a reference. 

  We will continue to keep this feature request in mind as we work to improve our somatic calling methods.

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