diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml
index 4127c9e0e..86760b8ab 100644
--- a/packages/GenomeAnalysisTK.xml
+++ b/packages/GenomeAnalysisTK.xml
@@ -21,14 +21,9 @@
       <class>org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker</class>
       <!-- Recalibration Covariates -->
       <class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class>
       <class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
       <class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
       <class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate</class>
       <class>org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate</class>
       <!-- Local realignment around indels -->
       <class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
@@ -49,6 +44,8 @@
       <class>org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance</class>
       <class>org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage</class>
       <class>org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun</class>
+      <class>org.broadinstitute.sting.gatk.walkers.annotator.MappingQualityZero</class>
+      <class>org.broadinstitute.sting.gatk.walkers.annotator.QualByDepth</class>
       <class>org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality</class>
       <class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class>
     </dependencies>
@@ -60,14 +57,9 @@
       <!-- Recalibration analysis script -->
       <class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</class>
       <class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class>
       <class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
       <class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
       <class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate</class>
       <class>org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate</class>
     </dependencies>
   </executable>