From e8bb88e33dba10e0092372d8edadbd32a3b8f05c Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 25 Nov 2009 18:08:12 +0000
Subject: [PATCH] Updated package for early access

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2158 348d0f76-0448-11de-a6fe-93d51630548a
---
 packages/GenomeAnalysisTK.xml | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml
index 17cb0c15b..25c732968 100644
--- a/packages/GenomeAnalysisTK.xml
+++ b/packages/GenomeAnalysisTK.xml
@@ -22,19 +22,20 @@
     <class>org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker</class>
     <class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperWalker</class>
     <class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker</class> 
+    <!-- Unified genotyper -->
+    <class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class>
     <!-- Variant filtration -->
     <class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class>
-    <!-- Single sample genotyper -->
-    <class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class>
-    <!-- And the filters -->
-    <class>org.broadinstitute.sting.gatk.walkers.filters.IVFSecondaryBases</class>
-    <class>org.broadinstitute.sting.gatk.walkers.filters.VECFisherStrand</class>
-    <class>org.broadinstitute.sting.gatk.walkers.filters.VECAlleleBalance</class>
-    <class>org.broadinstitute.sting.gatk.walkers.filters.VECDepthOfCoverage</class>
-    <class>org.broadinstitute.sting.gatk.walkers.filters.VECLodThreshold</class>
-    <class>org.broadinstitute.sting.gatk.walkers.filters.VECMappingQualityZero</class>
-    <class>org.broadinstitute.sting.gatk.walkers.filters.VECIndelArtifact</class>
-    <class>org.broadinstitute.sting.gatk.walkers.filters.VECClusteredSnps</class>
+    <!-- Variant annotator -->
+    <class>org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator</class>
+    <!-- And the annotations -->
+    <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.FisherStrand</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.RMSMappingQuality</class>
+    <class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class>
   </dependencies>
   <resources>
     <!-- GATK sample code and build scripts -->