Is GATK4 HaplotypeCaller in evaluation phase?

breardonbreardon Cambridge, MAMember, Broadie

Hi GATK team,

Congratulations on the release! I just found this public method in FireCloud that notes that HaplotypeCaller in GATK4 should not be used for production use yet since it is still in evaluation phase. This post was last updated on January 9th, the day of GATK4 release. Is this statement true? Could you provide more details about HaplotypeCaller evaluation?



  • breardonbreardon Cambridge, MAMember, Broadie
    edited January 31

    Edit: Sorry for the double comment!

  • breardonbreardon Cambridge, MAMember, Broadie

    The note is, on lines 17-19 of the WDL -

    IMPORTANT NOTE: HaplotypeCaller in GATK4 is still in evaluation phase and should not be used in production until it has been fully vetted. In the meantime, use the GATK3 version for any production needs.

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Broadie, Moderator admin

    Hi @breardon sorry for the delay. I believe this just wasn't updated, but let me double check with the team @KateN

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Brandon! Sorry for the delayed response, for some reason your question ended up in a section of the forum that is normally reserved for official docs so we don't monitor it for support. I'm moving it and will fix whatever permissions error led to this.

    To answer your question, that comment line is a leftover from pre-4.0 that was overlooked when we updated the WDLs. HaplotypeCaller in GATK4 is now considered production-worthy. We'll fix that, thanks for reporting it!

  • breardonbreardon Cambridge, MAMember, Broadie

    Ah, gotcha. Thank you everyone!

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