HaplotypeCaller on haploid genomes

RoddyPRoddyP Posts: 1Member
edited February 2013 in Ask the GATK team

I'm trying to run HaplotypeCaller on a haploid organism. Is this possible? What argument should I use for this?
My first attempt produced a diploid calls.

Sorry for the silly question

Post edited by Geraldine_VdAuwera on


  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,424Administrator, GATK Developer admin

    Currently the HaplotypeCaller only supports diploid calling. If you want to call non-diploid samples you'll need to use the UnifiedGenotyper.

    Geraldine Van der Auwera, PhD

  • KlausNZKlausNZ Posts: 45Member

    Geraldine, I wonder whether the Broad production pipelines processes sex chromosomes in male samples different than autosomes or sex chromosomes in female samples? I've read you're using both UG and HC, so are you ignoring the HC calls (if any)?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,424Administrator, GATK Developer admin

    Hi Klaus,

    We don't currently do anything special with the sex chromosomes in our production pipeline. This means that in male samples, X and Y get called as if they were diploid, so heterozygous calls should be thrown out. As far as I know, any researchers working on the sex chromosomes have their own approaches to dealing with this since it is a fairly specialized topic.

    Geraldine Van der Auwera, PhD

  • Muriel_GBMuriel_GB Univ. Fribourg, SwitzerlandPosts: 7Member

    One year after the question, I was wondering if this answer is still true ?
    HaplotypeCaller still only supports diploid calling ?
    Thanks a lot !

  • ebanksebanks Broad InstitutePosts: 684Member, Administrator, GATK Developer, Broadie, Moderator, DSDE Member, GP Member admin

    Yes, only diploid still. But we do have plans to work on this in the not too distant future.

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

  • tommycarstensentommycarstensen United KingdomPosts: 256Member ✭✭

    For anyone reading this thread now. HaplotypeCaller now has a --sample_ploidy argument.

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