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ReadBackedPhasing of somatic and germline variants?

RightOnTimeRightOnTime AmsterdamMember
edited February 2018 in Ask the GATK team

Hi all,

I'd like to know which germline variants are proximal to and on the same chromosome as detected somatic variants. Is there an out-of-the-box way to phase germline and somatic variants to one another? If not, do you see a role for GATK ReadBackedPhasing?

Thanks for your help and my apologies if this has been answered already, I couldn't find anything related.

-M

Answers

  • SheilaSheila Broad InstituteMember, Broadie admin

    @RightOnTime
    Hi M,

    There is currently no easy way to do this. Mutect2 only outputs the somatic sites. However, there are plans to have Mutect2 output both somatic and germline variants. That should be coming soonish.

    -Sheila

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