From e936cbff1b4298aa8112d7061b06abf0dda59973 Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 19 Jan 2010 21:29:43 +0000
Subject: [PATCH] Removed experimental recalibration covariates.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2631 348d0f76-0448-11de-a6fe-93d51630548a
---
 packages/GATK-GSA-Pipeline.xml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/packages/GATK-GSA-Pipeline.xml b/packages/GATK-GSA-Pipeline.xml
index 907e9713b..ac37491e7 100644
--- a/packages/GATK-GSA-Pipeline.xml
+++ b/packages/GATK-GSA-Pipeline.xml
@@ -15,12 +15,6 @@
     <dependencies>
       <!-- Filters -->
       <package>org.broadinstitute.sting.gatk.filters</package>
-      <!-- Recalibration Covariates -->
-      <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.PrimerRoundCovariate</class>
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate</class>
       <!-- From playground -->
       <class>org.broadinstitute.sting.playground.gatk.walkers.varianteval.VariantEvalWalker</class>
       <class>org.broadinstitute.sting.playground.gatk.walkers.contamination.FindContaminatingReadGroupsWalker</class>