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value of joint genotyping in trio's

matdmsetmatdmset GhentMember


We're looking into modernizing our workflows and I was wondering if there's much value to joint genotyping very small cohorts (e.g. trio's), as opposed to comparing results of three separate samples next to each other.

I'd like to know how much this could affect quality scores and actual genotypes etc. I can see the value for large cohorts, but I have my doubts with something as small as 3 individuals


Best Answer


  • matdmsetmatdmset GhentMember

    Thanks! That's all I needed to know!

  • GERGER Member

    Regarding the above, I have two questions:
    1) Are the results of running HaplotypeCaller on the 3 BAM files together the same as doing gvcf for each individually followed by GenotypeGVCFs?
    2) if the trio samples are exome samples, is it correct that one cannot do GVCF calling followed by GenotypeGVCFs, and the only way is to run HaplotypeCaller on the 3 BAM files? Because all of your cohort joint-calling pipeline state that at least 30 exomes are needed. Or is this limitation to > 30 exomes only due to the VQSR step and running GenotypeGVCfs on just 3 exome GVCFs is stlil ok?


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi ,

    The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal/erroneous results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

    Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

    We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

    For context, see this [announcement](https://software.broadinstitute.org/gatk/blog?id=24419 “announcement”) and check out our [support policy](https://gatkforums.broadinstitute.org/gatk/discussion/24417/what-types-of-questions-will-the-gatk-frontline-team-answer/p1?new=1 “support policy”).

  • matdmsetmatdmset GhentMember
    edited November 2019

    Hi @GER

    Interesting question! I'm curious what the support team (or anyone else ) has to say about this. We've been analyzing exome trio's using gvcf for a while now, it'd be great to know if we're doing something wrong somehow...


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