diff --git a/build.xml b/build.xml
index d640e6339..224bb6417 100644
--- a/build.xml
+++ b/build.xml
@@ -12,8 +12,8 @@
     <property name="queue.source.dir" value="scala/src" />
     <property name="queue.classes" value="${build.dir}/scala/classes" />
 
-    <property name="queue-gatk-extensions.source.dir" value="${build.dir}/queue-gatk-extensions/src" />
-    <property name="queue-gatk-extensions.classes" value="${build.dir}/queue-gatk-extensions/classes" />
+    <property name="queue-extensions.source.dir" value="${build.dir}/queue-extensions/src" />
+    <property name="queue-extensions.classes" value="${build.dir}/queue-extensions/classes" />
     
     <!-- where to find the tribble distro -->
     <property name="tribble.dir" value="tribble" />
@@ -66,8 +66,8 @@
         <pathelement location="${java.classes}" />
     </path>
 
-    <!-- Path to queue-gatk-extendsions dependencies. -->
-    <path id="queue-gatk-extensions.dependencies">
+    <!-- Path to queue-extendsions dependencies. -->
+    <path id="queue-extensions.dependencies">
         <path refid="runtime.dependencies" />
         <pathelement location="${java.classes}" />
         <pathelement location="${queue.classes}" />
@@ -113,7 +113,7 @@
     </target>
 
     <target name="init.buildall">
-        <!-- Set the properties needed to build Queue and the Queue GATK Extensions -->
+        <!-- Set the properties needed to build Queue -->
         <property name="gatk.target" value="oneoffs"/>
         <property name="queue.target" value="core"/>
     </target>
@@ -143,7 +143,7 @@
             <equals arg1="${env.QUEUE_BUILD_TYPE}" arg2="$${env.QUEUE_BUILD_TYPE}" />
         </condition>
 
-        <!-- If the queue target is set, or if the queue-gatk-extensions needs to be built, then include all queue tasks. -->
+        <!-- If the queue target is set, or if the queue-extensions needs to be built, then include all queue tasks. -->
         <condition property="queue.include">
             <or>
                 <not><equals arg1="${queue.target}" arg2="none" /></not>
@@ -211,21 +211,21 @@
     </target>
 
     <!-- NOTE: Extracting help first to avoid "Unable to load help text.  Help output will be sparse." warning message. -->
-    <target name="queue-gatk-extensions.generate" depends="gatk.compile, queue.compile, extracthelp" if="queue.include" description="generate GATK modules for Queue">
-        <mkdir dir="${queue-gatk-extensions.source.dir}"/>
+    <target name="queue-extensions.generate" depends="gatk.compile, queue.compile, extracthelp" if="queue.include" description="generate GATK modules for Queue">
+        <mkdir dir="${queue-extensions.source.dir}"/>
         <echo>Generating Queue GATK extensions...</echo>
-        <java fork="true" failonerror="true" classname="org.broadinstitute.sting.queue.extensions.gatk.GATKExtensionsGenerator" classpathref="queue-gatk-extensions.dependencies">
+        <java fork="true" failonerror="true" classname="org.broadinstitute.sting.queue.extensions.gatk.GATKExtensionsGenerator" classpathref="queue-extensions.dependencies">
             <arg value="-outDir" />
-            <arg path="${queue-gatk-extensions.source.dir}" />
+            <arg path="${queue-extensions.source.dir}" />
             <arg value="-l" />
             <arg value="WARN" />
         </java>
     </target>
 
-    <target name="queue-gatk-extensions.compile" depends="queue-gatk-extensions.generate" if="queue.include" description="compile GATK modules for Queue">
-        <mkdir dir="${queue-gatk-extensions.classes}"/>
+    <target name="queue-extensions.compile" depends="queue-extensions.generate" if="queue.include" description="compile extensions for Queue">
+        <mkdir dir="${queue-extensions.classes}"/>
         <echo>Building Queue GATK extensions...</echo>
-        <scalac srcdir="${queue-gatk-extensions.source.dir}" destdir="${queue-gatk-extensions.classes}" classpathref="queue-gatk-extensions.dependencies" deprecation="yes" unchecked="yes">
+        <scalac srcdir="${queue-extensions.source.dir}" destdir="${queue-extensions.classes}" classpathref="queue-extensions.dependencies" deprecation="yes" unchecked="yes">
             <include name="**/*.scala"/>
         </scalac>
     </target>
@@ -245,7 +245,7 @@
       </javadoc>
     </target>
 
-    <target name="sting.compile" depends="gatk.compile, queue.compile, queue-gatk-extensions.compile" />
+    <target name="sting.compile" depends="gatk.compile, queue.compile, queue-extensions.compile" />
 
     <target name="init.jar" depends="sting.compile,extracthelp">
         <mkdir dir="${dist.dir}"/>
@@ -295,21 +295,21 @@
 
     </target>
 
-    <target name="queue.jar" depends="queue.compile, queue-gatk-extensions.compile, init.jar" if="queue.include">
+    <target name="queue.jar" depends="queue.compile, queue-extensions.compile, init.jar" if="queue.include">
         <jar jarfile="${dist.dir}/Queue.jar">
             <fileset dir="${queue.classes}">
                 <include name="org/broadinstitute/sting/queue/**/*.class"/>
             </fileset>
+            <fileset dir="${java.classes}">
+              <include name="org/broadinstitute/sting/queue/**/*.class" />
+            </fileset>
+            <fileset dir="${queue-extensions.classes}">
+              <include name="**/*.class" />
+            </fileset>
             <manifest>
                 <attribute name="Main-Class" value="org.broadinstitute.sting.queue.QCommandLine" />
             </manifest>
         </jar>
-
-        <jar jarfile="${dist.dir}/QueueGATKExtensions.jar">
-          <fileset dir="${queue-gatk-extensions.classes}">
-            <include name="**/*.class" />
-          </fileset>
-        </jar>
     </target>
 
     <target name="sting.jar" depends="sting-utils.jar, gatk.jar, queue.jar" />
@@ -352,12 +352,6 @@
                 <attribute name="Class-Path" value="${jar.classpath}" />
             </manifest>
         </jar>
-
-        <jar jarfile="${dist.dir}/QueueGATKExtensions.jar" update="true" >
-            <manifest>
-                <attribute name="Class-Path" value="${jar.classpath}" />
-            </manifest>
-        </jar>
     </target>
 
     <target name="sting.manifests" depends="sting-utils.manifests, gatk.manifests, queue.manifests" />
@@ -556,7 +550,7 @@
         <delete dir="javadoc"/>
     </target>
 
-    <target name="javadoc" depends="init.buildall,resolve,queue-gatk-extensions.generate" description="generates javadoc">
+    <target name="javadoc" depends="init.buildall,resolve,queue-extensions.generate" description="generates javadoc">
       <mkdir dir="javadoc"/>
       <javadoc destdir="javadoc"
                classpathref="runtime.dependencies">
@@ -564,14 +558,11 @@
       </javadoc>
 
         <mkdir dir="javadoc/queue"/>
-        <scaladoc srcdir="${queue.source.dir}" destdir="javadoc/queue" classpathref="queue.dependencies" deprecation="yes" unchecked="yes">
+        <scaladoc srcdir="" destdir="javadoc/queue" classpathref="queue-extensions.dependencies" deprecation="yes" unchecked="yes">
+            <src path="${queue.source.dir}"/>
+            <src path="${queue-extensions.source.dir}"/>
             <include name="org/broadinstitute/sting/queue/**/*.scala"/>
         </scaladoc>
-
-        <mkdir dir="javadoc/queue-gatk-extensions"/>
-        <scaladoc srcdir="${queue-gatk-extensions.source.dir}" destdir="javadoc/queue-gatk-extensions" classpathref="queue-gatk-extensions.dependencies" deprecation="yes" unchecked="yes">
-            <include name="org/broadinstitute/sting/queue/extensions/**/*.scala"/>
-        </scaladoc>
     </target>
 
     <!-- Unzip all classes from their current locations and assemble them in a staging directory -->
diff --git a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index fe8821a61..33e8d3a22 100755
--- a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -171,7 +171,7 @@ public class GATKArgumentCollection {
     public IntervalMergingRule intervalMerging = IntervalMergingRule.ALL;
 
     @ElementList(required = false)
-    @Argument(fullName = "read_group_black_list", shortName="rgbl", doc="Filters out read groups matching <TAG>:<STRING> or a .txt file containing the filter strings one per line.", required = false)
+    @Input(fullName = "read_group_black_list", shortName="rgbl", doc="Filters out read groups matching <TAG>:<STRING> or a .txt file containing the filter strings one per line.", required = false)
     public List<String> readGroupBlackList = null;
 
     /**
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 153138768..ac8a1a384 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.indels;
 import net.sf.samtools.*;
 import net.sf.samtools.util.StringUtil;
 import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -44,8 +44,6 @@ import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.CommandLineUtils;
 
 import java.io.File;
 import java.io.FileWriter;
@@ -63,7 +61,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
     public static final String ORIGINAL_POSITION_TAG = "OP";
     public static final String PROGRAM_RECORD_NAME = "GATK IndelRealigner";
 
-    @Argument(fullName="targetIntervals", shortName="targetIntervals", doc="intervals file output from RealignerTargetCreator", required=true)
+    @Input(fullName="targetIntervals", shortName="targetIntervals", doc="intervals file output from RealignerTargetCreator", required=true)
     protected String intervalsFile = null;
 
     @Argument(fullName="LODThresholdForCleaning", shortName="LOD", doc="LOD threshold above which the cleaner will clean", required=false)
@@ -72,7 +70,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
     @Argument(fullName="entropyThreshold", shortName="entropy", doc="percentage of mismatches at a locus to be considered having high entropy", required=false)
     protected double MISMATCH_THRESHOLD = 0.15;
 
-    @Argument(fullName="output", shortName="O", required=false, doc="Output bam")
+    @Output(fullName="output", shortName="O", required=false, doc="Output bam")
     protected String writerFilename = null;
 
     @Argument(fullName="bam_compression", shortName="compress", required=false, doc="Compression level to use for output bams [default:5]")
@@ -115,15 +113,15 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
     // DEBUGGING OPTIONS FOLLOW
 
     @Hidden
-    @Argument(fullName="indelsFileForDebugging", shortName="indels", required=false, doc="Output file (text) for the indels found; FOR DEBUGGING PURPOSES ONLY")
+    @Output(fullName="indelsFileForDebugging", shortName="indels", required=false, doc="Output file (text) for the indels found; FOR DEBUGGING PURPOSES ONLY")
     protected String OUT_INDELS = null;
 
     @Hidden
-    @Argument(fullName="statisticsFileForDebugging", shortName="stats", doc="print out statistics (what does or doesn't get cleaned); FOR DEBUGGING PURPOSES ONLY", required=false)
+    @Output(fullName="statisticsFileForDebugging", shortName="stats", doc="print out statistics (what does or doesn't get cleaned); FOR DEBUGGING PURPOSES ONLY", required=false)
     protected String OUT_STATS = null;
 
     @Hidden
-    @Argument(fullName="SNPsFileForDebugging", shortName="snps", doc="print out whether mismatching columns do or don't get cleaned out; FOR DEBUGGING PURPOSES ONLY", required=false)
+    @Output(fullName="SNPsFileForDebugging", shortName="snps", doc="print out whether mismatching columns do or don't get cleaned out; FOR DEBUGGING PURPOSES ONLY", required=false)
     protected String OUT_SNPS = null;
 
     // the intervals input by the user
diff --git a/packages/Queue.xml b/packages/Queue.xml
index 951064070..c7a6dda72 100644
--- a/packages/Queue.xml
+++ b/packages/Queue.xml
@@ -11,8 +11,8 @@
             <package name="org.broadinstitute.sting.queue.function.*" />
             <package name="org.broadinstitute.sting.queue.util" />
 
-            <!-- Queue GATK Extensions -->
-            <package name="org.broadinstitute.sting.queue.extensions.gatk" />
+            <!-- Queue Extensions -->
+            <package name="org.broadinstitute.sting.queue.extensions.*" />
         </dependencies>
     </executable>
 </package>
diff --git a/scala/qscript/kshakir/CleanBamFile.scala b/scala/qscript/kshakir/CleanBamFile.scala
new file mode 100644
index 000000000..729cea827
--- /dev/null
+++ b/scala/qscript/kshakir/CleanBamFile.scala
@@ -0,0 +1,143 @@
+import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
+import org.broadinstitute.sting.queue.QScript
+import org.broadinstitute.sting.queue.extensions.gatk._
+
+class CleanBamFile extends QScript {
+  qscript =>
+
+  @Argument(doc="gatk jar", shortName="gatk")
+  var gatkJar: File = _
+
+  @Argument(doc="fix mates jar", shortName="fixMates")
+  var fixMatesJar: File = _
+
+  @Input(doc="Script that can merge text files, for example Sting/shell/mergeText.sh.", shortName="MTS")
+  var mergeTextScript: String = _
+
+  @Argument(doc="base name for output files", shortName="base")
+  var baseName: String = _
+
+  @Input(doc="reference genome", shortName="R")
+  var referenceFile: File = _
+
+  @Input(doc="recalibrated bam", shortName="I")
+  var recalibratedBam: File = _
+
+  @Argument(doc="read group blacklist conversion script that can convert firehose outputs to a GATK blacklist file.", shortName="RGBLS")
+  var readGroupBlackListScript: String = _
+
+  @Argument(doc="read group blacklist", shortName="RGBL", required=false)
+  var readGroupBlackList: String = _
+
+  @Argument(doc="intervals", shortName="L", required=false)
+  var intervals: File = _
+
+  @Argument(doc="Script that can split the interval file by contig, for example Sting/python/splitIntervalsByContig.py.", shortName="RTCSS")
+  var targetCreatorScatterScript: String = _
+
+  @Argument(doc="RealignerTargetCreator scatter count.  " +
+          "Best if it is either 1 or the number of contigs in the interval list.  " +
+          "If used the compute farm must also be used.", shortName="RTCSC")
+  var targetCreatorScatterCount = 0
+
+  @Argument(doc="Script that can split the intervals evenly, for example Sting/shell/splitIntervals.sh.", shortName="IRSS")
+  var indelRealignerScatterScript: String = _
+
+  @Argument(doc="IndelRealigner scatter count.", shortName="IRSC")
+  var indelRealignerScatterCount = 0
+
+  @Input(doc="dbsnp file", shortName="D")
+  var dbsnpFile: File = _
+
+  trait GATKCommonArgs extends CommandLineGATK {
+    this.jarFile = qscript.gatkJar
+    this.reference_sequence = qscript.referenceFile
+    this.intervals = qscript.intervals
+    this.input_file :+= recalibratedBam
+    this.cleanupTempDirectories = true
+  }
+
+  def baseFile(suffix: String) = new File(baseName + suffix)
+
+  def script = {
+    val blacklistConverter = new CommandLineFunction {
+      @Output(doc="blacklist file") var blacklistFile: File = _
+      def commandLine = readGroupBlackListScript + " " + blacklistFile + " " + readGroupBlackList
+    }
+
+    if (readGroupBlackList != null) {
+      blacklistConverter.blacklistFile = baseFile(".blacklist.txt")
+      add(blacklistConverter)
+    }
+
+    // -T RealignerTargetCreator -I <input.bam> -R <reference.genome> <interval.list> <blacklist.file> -o <base.name>.merged.intervals
+    val targetCreator = new RealignerTargetCreator with GATKCommonArgs
+    targetCreator.memoryLimit = Some(2)
+    targetCreator.read_group_black_list :+= blacklistConverter.blacklistFile
+    targetCreator.out = baseFile(".merged.intervals")
+    targetCreator.scatterCount = targetCreatorScatterCount
+    targetCreator.setupScatterFunction = {
+      case (scatter: IntervalScatterFunction, _) =>
+        scatter.splitIntervalsScript = targetCreatorScatterScript
+    }
+    targetCreator.setupGatherFunction = {
+      case (gather: SimpleTextGatherFunction, _) =>
+        gather.mergeTextScript = mergeTextScript
+    }
+
+    // -T IndelRealigner -I <input.bam> -R <reference.genome> <blacklist.file> -stats <base.name>.indel.stats
+    // -O <base.name>.unfixed.cleaned.bam -maxInRam 200000 -targetIntervals <merged.intervals> -D <dbsnp.file>
+    val realigner = new IndelRealigner with GATKCommonArgs
+    realigner.memoryLimit = Some(4)
+    realigner.read_group_black_list :+= blacklistConverter.blacklistFile
+    realigner.statisticsFileForDebugging = baseFile(".indel.stats")
+    realigner.maxReadsInRam = Some(200000)
+    realigner.targetIntervals = targetCreator.out
+    realigner.DBSNP = dbsnpFile
+    realigner.scatterCount = indelRealignerScatterCount
+
+    val bamIndex = new BamIndexFunction
+
+    if (realigner.scatterCount > 1) {
+      realigner.output = baseFile(".cleaned.bam")
+      // While gathering run fix mates.
+      realigner.setupScatterFunction = {
+        case (scatter: IntervalScatterFunction, _) =>
+          scatter.splitIntervalsScript = indelRealignerScatterScript
+      }
+      realigner.setupGatherFunction = {
+        case (gather: PicardBamJarFunction, _) =>
+          gather.memoryLimit = Some(4)
+          gather.jarFile = fixMatesJar
+          // Don't pass this AS=true to fix mates!
+          gather.assumeSorted = None
+        case (gather: SimpleTextGatherFunction, _) =>
+          gather.mergeTextScript = mergeTextScript
+      }
+
+      bamIndex.bamFile = realigner.output
+    } else {
+      realigner.output = baseFile(".unfixed.cleaned.bam")
+
+      // Explicitly run fix mates if the function won't be scattered.
+      var fixMates = new PicardBamJarFunction {
+        // Declare inputs/outputs for dependency tracking.
+        @Input(doc="unfixed bam") var unfixed: File = _
+        @Output(doc="fixed bam") var fixed: File = _
+        def inputBams = List(unfixed)
+        def outputBam = fixed
+      }
+      fixMates.memoryLimit = Some(4)
+      fixMates.jarFile = fixMatesJar
+      fixMates.unfixed = realigner.output
+      fixMates.fixed = baseFile(".cleaned.bam")
+
+      bamIndex.bamFile = fixMates.fixed
+
+      // Add the fix mates explicitly
+      add(fixMates)
+    }
+
+    add(targetCreator, realigner, bamIndex)
+  }
+}
diff --git a/scala/src/org/broadinstitute/sting/queue/QSettings.scala b/scala/src/org/broadinstitute/sting/queue/QSettings.scala
index 1ed32f1c7..b97bf176f 100644
--- a/scala/src/org/broadinstitute/sting/queue/QSettings.scala
+++ b/scala/src/org/broadinstitute/sting/queue/QSettings.scala
@@ -12,7 +12,7 @@ class QSettings {
   var jobNamePrefix: String = QSettings.processNamePrefix
 
   @Argument(fullName="job_queue", shortName="jobQueue", doc="Default queue for compute farm jobs.", required=false)
-  var jobQueue: String = "broad"
+  var jobQueue: String = _
 
   @Argument(fullName="job_project", shortName="jobProject", doc="Default project for compute farm jobs.", required=false)
   var jobProject: String = "Queue"
diff --git a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala
index 13ce477c4..8a442f6f5 100644
--- a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala
@@ -1,17 +1,14 @@
 package org.broadinstitute.sting.queue.extensions.gatk
 
-import org.broadinstitute.sting.queue.function.JarCommandLineFunction
-import org.broadinstitute.sting.commandline.Argument
 import org.broadinstitute.sting.queue.function.scattergather.GatherFunction
+import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
 
 /**
- * Merges BAM files using Picards MergeSampFiles.jar.
+ * Merges BAM files using Picards MergeSamFiles.jar.
  * At the Broad the jar can be found at /seq/software/picard/current/bin/MergeSamFiles.jar.  Outside the broad see http://picard.sourceforge.net/")
  */
-class BamGatherFunction extends GatherFunction with JarCommandLineFunction {
-  @Argument(doc="Compression level 1-9", required=false)
-  var compressionLevel: Option[Int] = None
-
-  override def commandLine = super.commandLine + "%s%s%s".format(
-    optional(" COMPRESSION_LEVEL=", compressionLevel), " AS=true VALIDATION_STRINGENCY=SILENT SO=coordinate OUTPUT=" + originalOutput, repeat(" INPUT=", gatherParts))
+class BamGatherFunction extends GatherFunction with PicardBamJarFunction {
+  this.assumeSorted = Some(true)
+  protected def inputBams = gatherParts
+  protected def outputBam = originalOutput
 }
diff --git a/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamJarFunction.scala b/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamJarFunction.scala
new file mode 100644
index 000000000..efd861f9b
--- /dev/null
+++ b/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamJarFunction.scala
@@ -0,0 +1,27 @@
+package org.broadinstitute.sting.queue.extensions.picard
+
+import org.broadinstitute.sting.queue.function.JarCommandLineFunction
+import java.io.File
+
+/**
+ * Wraps a Picard jar that operates on BAM files.
+ * See http://picard.sourceforge.net/ for more info.
+ *
+ * Since the jar files take slightly different arguments
+ * some values are optional.
+ */
+trait PicardBamJarFunction extends JarCommandLineFunction {
+  var validationStringency = "SILENT"
+  var sortOrder = "coordinate"
+  var compressionLevel: Option[Int] = None
+  var maxRecordsInRam: Option[Int] = None
+  var assumeSorted: Option[Boolean] = None
+
+  protected def inputBams: List[File]
+  protected def outputBam: File
+
+  override def commandLine = super.commandLine + "%s%s%s".format(
+    optional(" COMPRESSION_LEVEL=", compressionLevel), optional(" VALIDATION_STRINGENCY=", validationStringency),
+    optional(" SO=", sortOrder), optional( " MAX_RECORDS_IN_RAM=", maxRecordsInRam), optional(" ASSUME_SORTED=", assumeSorted),
+    " OUTPUT=" + outputBam, repeat(" INPUT=", inputBams), " TMP_DIR=" + jobTempDir)
+}