Where can I get AnalyzeCovariates.jar

Irsan_KooiIrsan_Kooi Posts: 1Member
edited January 2013 in Ask the GATK team

Hi all,

I have just downloaded the GATK 2.2.3 from broad but I cant find the AnalyzeCovariates.jar file, where can I get it?


Post edited by Geraldine_VdAuwera on


  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 9,980Administrator, Dev admin

    Hi there,

    AnalyzeCovariates is no longer included in the GATK since version 2.0. Now to do base recalibration you use BaseRecalibration and PrintReads. Please see the documentation for details on how to use the new tools.

    Geraldine Van der Auwera, PhD

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