Does GATK4 Mutect2 support Force Calling?

cbaocbao Member, Broadie ✭✭

Hi,
Does GATK4 Mutect2 support Force Calling? If yes, could you let me know how to do it? Thanks a lot!

Thanks,
Chunyang

Tagged:

Issue · Github
by shlee

Issue Number
4555
State
closed
Last Updated
Assignee
Array
Closed By
sooheelee

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Answers

  • cbaocbao Member, Broadie ✭✭

    Thanks @shlee,

    Say that we have some known variants (e.g. VCF file from GATK4 mutect2) in sample A and want to force them to call mutations in sample B. The key is to determine the genotype of sample B by the intervals of these variants. In the research of cancer evolution, it is important to figure out whether the mutations in late grade samples are "true negative" or just filtered out in early grade samples. That is the main reason why I want to run force calling. I really appreciate your help!

    Best,
    Chunyang

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