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