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HaplotypeCaller on haploid genomes

RoddyPRoddyP Member Posts: 2
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 Administrator, Dev Posts: 10,690 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 Member Posts: 58

    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 Administrator, Dev Posts: 10,690 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, SwitzerlandMember Posts: 7

    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 InstituteMember, Administrator, Broadie, Moderator, Dev Posts: 698 admin

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

    Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

  • tommycarstensentommycarstensen United KingdomMember Posts: 400 ✭✭✭

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

  • kshitij_tandonkshitij_tandon TaipeiMember Posts: 12

    is it --sample_ploidy or -ploidy for HC inorder to use it for Haploid Organism..Please reply ASAP

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,690 admin

    @kshitij_tandon Please think about how it sounds when you ask for a reply "ASAP". Think about how many people are asking questions, and how it's likely that most of them are waiting for an answer in order to be able to move on with their work. In that context, do you think that asking for a reply "ASAP" will get you priority service? Do you think it should?

    Geraldine Van der Auwera, PhD

  • JeegarJeegar CanadaMember Posts: 16

    Just to confirm. In case of Haploid organism argument for variant calling with Haplotype caller will involve '-ploidy 1'.??

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