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HaplotypeCaller --output_mode / -out_mode

tommycarstensentommycarstensen United KingdomMember ✭✭✭

UnifiedGenotyper supports --output_mode EMIT_ALL_SITES (default EMIT_VARIANTS_ONLY). Will HaplotypeCaller have a similar option in the future?

Best Answer


  • tommycarstensentommycarstensen United KingdomMember ✭✭✭

    Gerladine, thank you for answering my question and pointing me to gVCF. According to the documentation it currently only works for single sample calling. I like UG --output_mode, because it can be combined with for example --alleles GENOTYPE_GIVEN_ALLELES. This is useful when doing "single population calling" and merging those VCF files after variant calling with CombineVariants. Thanks again.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Tommy,

    That makes sense. Unfortunately we're sort of sitting in between two chairs right now with HaplotypeCaller; we're working on complementary features to enable this functionality in the context of multi-sample/population studies, but in the meantime we had to deactivate the emit-all function. Sorry for the inconvenience!

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