diff --git a/packages/AnalyzeCovariatesModule.xml b/packages/AnalyzeCovariatesModule.xml
new file mode 100644
index 000000000..f5b0d79b9
--- /dev/null
+++ b/packages/AnalyzeCovariatesModule.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<package>
+  <name>AnalyzeCovariates</name>
+  <executable>
+    <name>AnalyzeCovariates</name>
+    <main-class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</main-class>
+    <dependencies>
+      <!-- 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.QualityScoreCovariate</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.TileCovariate</class>
+    </dependencies>
+  </executable>
+</package>
diff --git a/packages/CreatePackager.xsl b/packages/CreatePackager.xsl
index b5e618cef..9cf2c63e2 100644
--- a/packages/CreatePackager.xsl
+++ b/packages/CreatePackager.xsl
@@ -32,28 +32,12 @@
       <!-- Create an output directory for the package -->
       <mkdir dir="{$package.dir}"/>
 
-      <xsl:for-each select="executable">
-	<!-- Create a jar file containing the specified classes / packages and all their dependencies -->
-	<jar jarfile="{concat($package.dir,name,'.jar')}">
-          <classfileset dir="{$staging.dir}">
-            <root classname="{main-class}"/>
-            <xsl:for-each select="dependencies/package">
-              <rootfileset dir="{$staging.dir}" includes="{concat(translate(current(),'.','/'),'/','*.class')}" />
-            </xsl:for-each>
-            <xsl:for-each select="dependencies/class">
-              <root classname="{current()}" />
-            </xsl:for-each>
-          </classfileset>
-          <xsl:for-each select="dependencies/properties">
-            <fileset file="{$staging.dir}/{current()}" />
-          </xsl:for-each>
-          <xsl:for-each select="dependencies/file">
-            <fileset file="{$staging.dir}/{current()}" />
-          </xsl:for-each>
-          <manifest>
-            <attribute name="Main-Class" value="{main-class}"/>
-          </manifest>
-	</jar>
+      <!-- Create the executable sections -->
+      <xsl:apply-templates select="executable" />
+
+      <!-- Add in other modules -->
+      <xsl:for-each select="module">
+	<xsl:apply-templates select="document(current())/package/executable" />
       </xsl:for-each>
 
       <!-- Include various script files -->
@@ -97,6 +81,39 @@
   <symlink link="{concat($target.dir,'/',$short.name)}" resource="{$full.path}" overwrite="true" />
 </xsl:template>
 
+<xsl:template match="executable">
+  <!-- Create a jar file containing the specified classes / packages and all their dependencies -->
+  <jar jarfile="{concat($package.dir,name,'.jar')}">
+    <classfileset dir="{$staging.dir}">
+      <root classname="{main-class}"/>
+    </classfileset>
+    <xsl:for-each select="properties">
+      <fileset file="{$staging.dir}/{current()}" />
+    </xsl:for-each>
+    <xsl:for-each select="module">
+      <xsl:apply-templates select="document(current())/package/executable/dependencies" />
+    </xsl:for-each>
+    <xsl:apply-templates select="dependencies" />
+    <manifest>
+      <attribute name="Main-Class" value="{main-class}"/>
+    </manifest>
+  </jar>
+</xsl:template>
+
+<xsl:template match="dependencies">
+  <classfileset dir="{$staging.dir}">
+    <xsl:for-each select="package">
+      <rootfileset dir="{$staging.dir}" includes="{concat(translate(current(),'.','/'),'/','*.class')}" />
+    </xsl:for-each>
+    <xsl:for-each select="class">
+      <root classname="{current()}" />
+    </xsl:for-each>
+  </classfileset>
+  <xsl:for-each select="file">
+    <fileset file="{$staging.dir}/{current()}" />
+  </xsl:for-each>
+</xsl:template>
+
 <!-- Determine the short name (filename w/o directory structure of the given filename -->
 <xsl:template name="get-short-name">
   <xsl:param name="string"/>
diff --git a/packages/GATK-GSA-Pipeline.xml b/packages/GATK-GSA-Pipeline.xml
index 9181d2382..907e9713b 100644
--- a/packages/GATK-GSA-Pipeline.xml
+++ b/packages/GATK-GSA-Pipeline.xml
@@ -6,46 +6,21 @@
   <executable>
     <name>GATK-GSA-Pipeline</name>
     <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
+    <properties>StingText.properties</properties>
+    <module>QualityScoresRecalibrationModule.xml</module>
+    <module>LocalRealignmentAroundIndelsModule.xml</module>
+    <module>UnifiedGenotyperModule.xml</module>
+    <module>VariantFiltrationModule.xml</module>
+    <module>VariantAnnotatorModule.xml</module>
     <dependencies>
-      <!-- Text extracted from the javadocs -->
-      <properties>StingText.properties</properties>
       <!-- Filters -->
       <package>org.broadinstitute.sting.gatk.filters</package>
-      <!-- Quality scores recalibration -->
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
-      <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>
-      <class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker</class>
-      <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>
-      <!-- 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.HomopolymerRun</class>
-      <class>org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality</class>
-      <class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class>
       <!-- From playground -->
       <class>org.broadinstitute.sting.playground.gatk.walkers.varianteval.VariantEvalWalker</class>
       <class>org.broadinstitute.sting.playground.gatk.walkers.contamination.FindContaminatingReadGroupsWalker</class>
diff --git a/packages/GATK-Picard.xml b/packages/GATK-Picard.xml
index 096fd54ed..0df3a57f1 100644
--- a/packages/GATK-Picard.xml
+++ b/packages/GATK-Picard.xml
@@ -7,9 +7,13 @@
   <executable>
     <name>GATK-Picard</name>
     <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
+    <properties>StingText.properties</properties>
+    <module>QualityScoresRecalibrationModule.xml</module>
+    <module>LocalRealignmentAroundIndelsModule.xml</module>
+    <module>UnifiedGenotyperModule.xml</module>
+    <module>VariantFiltrationModule.xml</module>
+    <module>VariantAnnotatorModule.xml</module>
     <dependencies>
-      <!-- Text extracted from the javadocs -->
-      <properties>StingText.properties</properties>
       <!-- Filters -->
       <package>org.broadinstitute.sting.gatk.filters</package>
       <class>org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker</class>
@@ -18,41 +22,12 @@
       <class>org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker</class>
       <class>org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker</class>
       <class>org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker</class>
-      <!-- Quality scores recalibration -->
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
-      <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.TileCovariate</class>
       <class>org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate</class>
-      <!-- Local realignment around indels -->
-      <class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
-      <class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker</class>
-      <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>
-      <!-- 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.HomopolymerRun</class>
-      <class>org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality</class>
-      <class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class>
     </dependencies>
   </executable>
   <resources>
diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml
index 5c5d3f58e..166cc3355 100644
--- a/packages/GenomeAnalysisTK.xml
+++ b/packages/GenomeAnalysisTK.xml
@@ -4,9 +4,14 @@
   <executable>
     <name>GenomeAnalysisTK</name>
     <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
+    <properties>StingText.properties</properties>
+    <module>QualityScoresRecalibrationModule.xml</module>
+    <module>LocalRealignmentAroundIndelsModule.xml</module>
+    <module>UnifiedGenotyperModule.xml</module>
+    <module>VariantFiltrationModule.xml</module>
+    <module>VariantAnnotatorModule.xml</module>
+    <module>VCFValidatorModule.xml</module>
     <dependencies>
-      <!-- Text extracted from the javadocs -->
-      <properties>StingText.properties</properties>
       <!-- Filters -->
       <package>org.broadinstitute.sting.gatk.filters</package>
       <!-- Basic qc walkers -->
@@ -16,40 +21,6 @@
       <class>org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker</class>
       <class>org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker</class>
       <class>org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker</class>
-      <!-- Quality scores recalibration -->
-      <class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
-      <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.QualityScoreCovariate</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.TileCovariate</class>
-      <!-- Local realignment around indels -->
-      <class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
-      <class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker</class>
-      <class>org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker</class>
-      <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>
-      <!-- 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.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>
-      <!-- VCF validator -->
-      <class>org.broadinstitute.sting.gatk.walkers.qc.VCFValidator</class>
     </dependencies>
   </executable>
   <executable>
diff --git a/packages/LocalRealignmentAroundIndelsModule.xml b/packages/LocalRealignmentAroundIndelsModule.xml
new file mode 100644
index 000000000..cca71ff63
--- /dev/null
+++ b/packages/LocalRealignmentAroundIndelsModule.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<package>
+  <name>LocalRealignmentAroundIndels</name>
+  <executable>
+    <name>LocalRealignmentAroundIndels</name>
+    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
+    <dependencies>
+      <!-- Local realignment around indels -->
+      <class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
+      <class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker</class>
+      <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> 
+    </dependencies>
+  </executable>
+</package>
diff --git a/packages/QualityScoresRecalibrationModule.xml b/packages/QualityScoresRecalibrationModule.xml
new file mode 100644
index 000000000..8e6dc6eab
--- /dev/null
+++ b/packages/QualityScoresRecalibrationModule.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<package>
+  <name>QualityScoresRecalibration</name>
+  <executable>
+    <name>QualityScoresRecalibration</name>
+    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
+    <dependencies>
+      <!-- Quality scores recalibration -->
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
+      <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.QualityScoreCovariate</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.TileCovariate</class>
+    </dependencies>
+  </executable>
+</package>
diff --git a/packages/UnifiedGenotyperModule.xml b/packages/UnifiedGenotyperModule.xml
new file mode 100644
index 000000000..2180fefc4
--- /dev/null
+++ b/packages/UnifiedGenotyperModule.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<package>
+  <name>UnifiedGenotyper</name>
+  <executable>
+    <name>UnifiedGenotyper</name>
+    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
+    <dependencies>
+      <!-- Unified genotyper -->
+      <class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class>
+    </dependencies>
+  </executable>
+</package>
diff --git a/packages/VCFValidatorModule.xml b/packages/VCFValidatorModule.xml
new file mode 100644
index 000000000..ea951fe46
--- /dev/null
+++ b/packages/VCFValidatorModule.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<package>
+  <name>VCFValidator</name>
+  <executable>
+    <name>VCFValidator</name>
+    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
+    <dependencies>
+      <!-- VCF validator -->
+      <class>org.broadinstitute.sting.gatk.walkers.qc.VCFValidator</class>
+    </dependencies>
+  </executable>
+</package>
diff --git a/packages/VariantAnnotatorModule.xml b/packages/VariantAnnotatorModule.xml
new file mode 100644
index 000000000..d2014b23a
--- /dev/null
+++ b/packages/VariantAnnotatorModule.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<package>
+  <name>VariantAnnotator</name>
+  <executable>
+    <name>VariantAnnotator</name>
+    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
+    <dependencies>
+      <!-- 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.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>
+  </executable>
+</package>
diff --git a/packages/VariantFiltrationModule.xml b/packages/VariantFiltrationModule.xml
new file mode 100644
index 000000000..6e423c5bf
--- /dev/null
+++ b/packages/VariantFiltrationModule.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<package>
+  <name>VariantFiltration</name>
+  <executable>
+    <name>VariantFiltration</name>
+    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
+    <dependencies>
+      <!-- Variant filtration -->
+      <class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class>
+    </dependencies>
+  </executable>
+</package>