From aa08c82ac056f7ab7858ce7e07d31d12649984fd Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 17 Jan 2010 02:17:32 +0000
Subject: [PATCH] Removed experimental covariates and added standard
 annotations.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2617 348d0f76-0448-11de-a6fe-93d51630548a
---
 packages/GenomeAnalysisTK.xml | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

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>