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newbie16newbie16 Member
edited July 2012 in Ask the GATK team

I am trying to execute CountCovariates in GATK Version 2.0 Lite. It seems that this walker is missing? I get the following error:

ERROR MESSAGE: Could not find walker with name: CountCovariates


Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Accepted Answer

    Hi there,

    Base Quality Score Recalibration no longer uses CountCovariates in GATK 2.0. This process is now done with a dedicated tool called BaseRecalibrator followed by PrintReads. You can find more details in the Methods And Workflows section of the Guide.

  • pwhiteusapwhiteusa Member

    In a separate thread (http://gatk.vanillaforums.com/discussion/comment/202/#Comment_202) you stated " GATK 2.0 Lite contains everything that was in 1.6, and is the continuation of the 1.6 development branch". While there may have been good reasons to replace CountCovariates, I don't think it is true to say the lite version is a continuation of 1.6 when implementation of BaseRecalibrator represents a significant change in our standard work flow. Are the other major differences between 1.6 and 2 Lite that we should be aware of?

  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭

    The Lite version of BaseRecalibrator is exactly the same thing as the old CountCovariates. It was renamed because the full 2.0 version has powerful extensions for recalibrating indels. Unless the renaming of a tool represents a significant change in your workflow, you should be okay here. No other changes to the standard tools other than extensions available in the full version (e.g. ploidy generalizations in the Unified Genotyper).

  • I do not think this is a good idea to change an "API-like" functions name. We users just want to use it, not controled by the tools.
    I hope all the functions and its name should not be changed if possible.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Such tool name changes are very rare; in this case, the change was part of a major version transition (1.x to 2.x). Please understand that we cannot keep every single tool name unchanged through such a major transition; that would be like holding the future hostage to the past. We developers do our best to minimize disruptions for our users (for example by documenting all important changes), but we cannot treat the tools as if they were carved in stone, otherwise we would never be able to bring you major improvements.

  • HeidihuangHeidihuang ChinaMember

    Excuse me, where can I find the documentation of CountVariates and TableRecalibration? I can't find them in the technical documentations?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Those tools have been replaced; please see the Base Recalibration documentation for details.

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