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Applying GATK to microbiome data

confuriousconfurious CaliforniaMember

Hi, I am interested in knowing how to apply gatk tools to microbiome data. Specifically, I would like to override the assumption of ploidy in the HaplotypeCaller and making it flexible, in that one sample could have a unknown number of haplotypes at the same time, I know somatic mutation caller Mutect2 does not share the assumption but then it's designed to specifically deal with normal - tumor sample pair which is not really applicable in the microbiome studies. Thanks

Issue · Github
by shlee

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  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭
    edited May 2017

    Hi @confurious, I'll let our MuTect developers know that this is a feature of interest to the microbiome community. Btw, the MuTect2 tool doc says:

    Tumor-only variant calling is possible but it is NOT supported and we will not answer any questions about it until it becomes a supported feature.

  • davidbendavidben BostonMember, Broadie, Dev ✭✭✭

    @confurious This has been on the shelf for a while but we're starting to support more off-label uses of Mutect2. I would be very curious to see how well simply running in tumor-only mode works. I would also be interested to know what sorts of new features and outputs in Mutect2 you might want to see for microbiome calling.

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