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Triggering genotype calls at HapMap sites

genegene Member Posts: 17
edited September 2012 in Ask the GATK team


I would like to trigger calls at HapMap sites even if they are HOM_REF in my sample. I used to accomplish this in an older GATK version with the following parameter passed to the UnifiedGenotyper: -B:trigger,VCF hapmap.vcf
Right now I am using version 1.6 of the GATK.
How could I accomplish exactly the same with this new version?

What I am trying to do (when doing VariantEval on the detected SNPs) is to obtain GenotypeConcordance for all:
Currently I only get the concordance values for HETs and HOM_VAR on the VariantEval output.
Asked in a different way, how could I get the 'n_true_HOM_REF_called_*' fields populated in the VariantEval?

Thanks for your help,

Post edited by Geraldine_VdAuwera on


  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,738 admin

    Hi Gene, please have a look at the documentation for the UnifiedGenotyper, specifically the --output_mode argument.

    Geraldine Van der Auwera, PhD

  • genegene Member Posts: 17

    Hi Geraldine,

    Thanks for your reply.

    • If I set --output_mode to EMIT_ALL_SITES I get the calls at HapMap HOM_REF sites but also every single base in the intervals indicated by -L file.bed gets called. This is undesirable.
      The previous -B:trigger,VCF hapmap.vcf argument would trigger aditional calls ONLY at those site that were HOM_REF in the HapMap reference. Is there a way to obtain this same effect with a different combination of parameters (without having to call SNPs at every single base)?


  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,738 admin

    Hi Gene,

    Sorry, I misunderstood what you are trying to do -- I thought you were using the HapMap call positions as intervals, to only make calls for those loci. If you want to also have the variant calls in the rest of the exome, you'll need to do it in a separate run, then merge the two VCFs. We no longer provide a way to do it all at once, sorry.

    Geraldine Van der Auwera, PhD

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