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haplotypecaller doesn't emit genotype at all sites

beckyzhapbeckyzhap Member Posts: 2
edited October 2012 in Ask the GATK team

I've tried to get genotype for all sites provided in interval file using haplotypeCaller. If using unifiedGenotyper, I can get the result by setting "output_mode EMIT_ALL_SITES". But haplotypeCaller doesn't report as expected by "output_mode EMIT_ALL_SITES". Even though I set "genotypeFullActiveRegion" or "fullHaplotype", haplotypeCaller doesn't seem to emit genotype at all sites. How to get desirable result using haplotypeCaller?

Post edited by Geraldine_VdAuwera on


  • lucdhlucdh Member Posts: 10

    Hi GATK team,
    Could it be this issue has not been resolved in GATK v 2.2.4? At least my recent attempts at getting HaplotypeCaller to report both variant and reference calls have failed, where UnifiedGenotyper with identical parameters works fine.

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,118 admin

    This question has been asked and answered previously. Basically this cannot currently be done with HaplotypeCaller. We are working on it but we can't give you an ETA on when it will be possible.

    Geraldine Van der Auwera, PhD

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