Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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

Answers

  • 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!

Sign In or Register to comment.