Haplotype caller

evanievani Posts: 3Member
edited July 2012 in Ask the GATK team


The version of GATK i have installed is unable to find command "HaplotypeCaller", i have the following versions of GATK installed.
version 2.0-0-gb142977 (built from git)
version 2.0-0-g4c0ffd4 (GenomeAnalysisTKLite.jar)
version 1.6-13-g91f02df

Errors out saying cannot find walker with name HaplotypeCaller.


Post edited by Carneiro on


  • ebanksebanks Broad InstitutePosts: 689Member, Administrator, GATK Dev, Broadie, Moderator, DSDE Dev, GP Member admin

    Hi Uday,

    The HaplotypeCaller is available only in the full release of the GATK (starting from 2.0), whereas you only have the lite version. I've just pushed in a patch so that in the future you will get a warning stating this when trying to use full-version-only walkers from the lite build of the GATK.

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

  • evanievani Posts: 3Member

    Is version 2.0 released ? If not when do you think it will be released ? Also if i have a version of GATK built from git, should that be containing this walker.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,171Administrator, GATK Dev admin

    Version 2.0 has been released, yes; please see the Downloads page for links to the available packages.

    The public git repository contains the source corresponding to GATK Lite, which does not contain the HaplotypeCaller walker. If you want to use it, you need to download the full version, but be aware its use is limited to non-commercial purposes at this time. Please see the GATK 2.0 Announcement on this forum for details.

    Geraldine Van der Auwera, PhD

  • evanievani Posts: 3Member

    I am sorry but i was unable to find version 2.0 . I looked at the download page and ftp



    May be i am looking in the wrong place, could you please point me in the rite direction.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,171Administrator, GATK Dev admin

    You need to look on the new website -- you should see the navigation bar at the top of this page. All downloads are clearly marked on the Downloads page.


    Geraldine Van der Auwera, PhD

  • williamwwilliamw North CarolinaPosts: 2Member

    Is the haplotype caller going to be added to the git repository at some point?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,171Administrator, GATK Dev admin

    Hi @williamw,

    The HC is available in the gatk-protected repository here: https://github.com/broadgsa/gatk-protected

    Geraldine Van der Auwera, PhD

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