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Can GATK mutect2 detect MNPs?

In GATK 3.8, we used readbackedphasing to merge SNPs into a MNP, but I did not see this tool listed for 4.0
Does mutect2 do this now?
Thanks

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @ugabronco
    Hi,

    There is no tool in GATK4 to merge MNPs. You will need to look outside of GATK or use version 3.8. Note, there are plans to make a tool that does this, but it has not been implemented yet.

    -Sheila

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