diff --git a/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java b/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
index 05088f186..5c48db670 100755
--- a/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
+++ b/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
@@ -377,11 +377,11 @@ public class ParsingEngine {
      * Extract all the argument sources from a given object, along with their bindings if obj != null .
      * @param obj the object corresponding to the sourceClass
      * @param sourceClass class to act as sources for other arguments.
-     * @param parentFields
+     * @param parentFields Parent Fields
      * @return A map of sources associated with this object and its aggregated objects and bindings to their bindings values
      */
     private static Map<ArgumentSource, Object> extractArgumentBindings(Object obj, Class sourceClass, Field[] parentFields) {
-        Map<ArgumentSource, Object> bindings = new HashMap<ArgumentSource, Object>();
+        Map<ArgumentSource, Object> bindings = new LinkedHashMap<ArgumentSource, Object>();
 
         while( sourceClass != null ) {
             Field[] fields = sourceClass.getDeclaredFields();
diff --git a/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java b/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
index 8e1324ebe..f059471a4 100644
--- a/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
+++ b/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
@@ -25,6 +25,7 @@
 package org.broadinstitute.sting.queue.extensions.gatk;
 
 import net.sf.samtools.SAMFileWriter;
+import org.broad.tribble.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.*;
 
 import java.io.File;
@@ -59,15 +60,15 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
             return "";
         else
             return String.format("%n" +
-                    "/** %n" +
-                    " *  Short name of %1$s%n" +
-                    " *  @return Short name of %1$s%n" +
+                    "/**%n" +
+                    " * Short name of %1$s%n" +
+                    " * @return Short name of %1$s%n" +
                     " */%n" +
                     "def %3$s = this.%1$s%n" +
                     "%n" +
-                    "/** %n" +
-                    " *  Short name of %1$s%n" +
-                    " *  @param value Short name of %1$s%n" +
+                    "/**%n" +
+                    " * Short name of %1$s%n" +
+                    " * @param value Short name of %1$s%n" +
                     " */%n" +
                     "def %4$s(value: %2$s) = this.%1$s = value%n",
                     getFieldName(),
@@ -96,7 +97,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
     }
 
     @Override
-    protected String getScatterGatherAnnotation() {
+    protected String getGatherAnnotation() {
         return "";
     }
 
@@ -120,9 +121,8 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
 
     private static List<? extends ArgumentField> getArgumentFields(ArgumentDefinition argumentDefinition) {
         if (intervalFields.contains(argumentDefinition.fullName) && argumentDefinition.ioType == ArgumentIOType.INPUT) {
-            boolean scatter = "intervals".equals(argumentDefinition.fullName);
             return Arrays.asList(
-                    new IntervalFileArgumentField(argumentDefinition, scatter),
+                    new IntervalFileArgumentField(argumentDefinition),
                     new IntervalStringArgumentField(argumentDefinition));
 
         // ROD Bindings are set by the RodBindField
@@ -166,18 +166,10 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
     }
 
     // if (intervalFields.contains(argumentDefinition.fullName) && argumentDefinition.ioType == ArgumentIOType.INPUT)
-    // Change intervals to an input file, and optionally scatter it.
+    // Change intervals exclusize of intervalsString.
     private static class IntervalFileArgumentField extends InputArgumentField {
-        private final boolean scatter;
-        public IntervalFileArgumentField(ArgumentDefinition argumentDefinition, boolean scatter) {
+        public IntervalFileArgumentField(ArgumentDefinition argumentDefinition) {
             super(argumentDefinition);
-            this.scatter = scatter;
-        }
-
-        @Override protected boolean isMultiValued() { return !this.scatter && super.isMultiValued(); }
-        @Override public boolean isScatter() { return this.scatter; }
-        @Override protected String getScatterGatherAnnotation() {
-            return scatter ? String.format("@Scatter(classOf[IntervalScatterFunction])%n") : super.getScatterGatherAnnotation();
         }
 
         @Override
@@ -241,10 +233,15 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
         @Override protected String getDefaultValue() { return "_"; }
 
         @Override public boolean isGather() { return true; }
-        @Override protected String getScatterGatherAnnotation() {
-            return String.format(SAMFileWriter.class.isAssignableFrom(argumentDefinition.argumentType)
-                ? "@Gather(classOf[BamGatherFunction])%n"
-                : "@Gather(classOf[org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction])%n");
+        @Override protected String getGatherAnnotation() {
+            String gather;
+            if (SAMFileWriter.class.isAssignableFrom(argumentDefinition.argumentType))
+                gather = "@Gather(classOf[BamGatherFunction])%n";
+            else if (VCFWriter.class.isAssignableFrom(argumentDefinition.argumentType))
+                gather = "@Gather(classOf[VcfGatherFunction])%n";
+            else
+                gather = "@Gather(classOf[org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction])%n";
+            return String.format(gather);
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java b/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
index 88ad2a02b..e5a6e86c2 100644
--- a/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
+++ b/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
@@ -72,7 +72,7 @@ public abstract class ArgumentField {
                 isRequired(),
                 getExclusiveOf(),
                 getValidation(),
-                getScatterGatherAnnotation(), getFieldName(), getFieldType(), getDefaultValue(),
+                getGatherAnnotation(), getFieldName(), getFieldType(), getDefaultValue(),
                 getDefineAddition());
     }
 
@@ -105,8 +105,8 @@ public abstract class ArgumentField {
     /** @return A validation string for the argument. */
     protected String getValidation() { return ""; }
 
-    /** @return A scatter or gather annotation with a line feed, or "". */
-    protected String getScatterGatherAnnotation() { return ""; }
+    /** @return A gather annotation with a line feed, or "". */
+    protected String getGatherAnnotation() { return ""; }
 
     // Scala
 
@@ -136,9 +136,6 @@ public abstract class ArgumentField {
         return importClasses;
     }
 
-    /** @return True if this field uses @Scatter. */
-    public boolean isScatter() { return false; }
-
     /** @return True if this field uses @Gather. */
     public boolean isGather() { return false; }
 
diff --git a/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java b/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
index a6893636e..6c77cc7f5 100644
--- a/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
+++ b/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
@@ -38,6 +38,7 @@ import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
@@ -104,7 +105,7 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
                 String clpClassName = clpManager.getName(clp);
 
                 writeClass("org.broadinstitute.sting.queue.function.JarCommandLineFunction", COMMANDLINE_PACKAGE_NAME, clpClassName,
-                        "", ArgumentDefinitionField.getArgumentFields(clp));
+                        false, "", ArgumentDefinitionField.getArgumentFields(clp));
 
                 if (clp == CommandLineGATK.class) {
                     for (Entry<String, Collection<Class<? extends Walker>>> walkersByPackage: walkerManager.getWalkerNamesByPackage(false).entrySet()) {
@@ -116,9 +117,16 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
                             argumentFields.addAll(RodBindField.getRodArguments(walkerType, trackBuilder));
                             argumentFields.addAll(ReadFilterField.getFilterArguments(walkerType));
 
+                            String constructor = String.format("analysisName = \"%1$s\"%nanalysis_type = \"%1$s\"%n", walkerName);
+                            String scatterClass = getScatterClass(walkerType);
+                            boolean isScatter = false;
+                            if (scatterClass != null) {
+                                isScatter = true;
+                                constructor += String.format("scatterClass = classOf[%s]%n", scatterClass);
+                            }
+
                             writeClass(COMMANDLINE_PACKAGE_NAME + "." + clpClassName, WALKER_PACKAGE_NAME, walkerName,
-                                    String.format("analysisName = \"%1$s\"%nanalysis_type = \"%1$s\"%n", walkerName),
-                                    argumentFields);
+                                    isScatter, constructor, argumentFields);
                         }
                     }
                 }
@@ -149,15 +157,22 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
         return false;
     }
 
-    private void writeClass(String baseClass, String packageName, String className, String constructor,
-                            List<? extends ArgumentField> argumentFields) throws IOException {
-        String content = getContent(CLASS_TEMPLATE, baseClass, packageName, className, constructor, "", argumentFields);
+    private String getScatterClass(Class<? extends Walker> walkerType) {
+        if (ReadWalker.class.isAssignableFrom(walkerType))
+            return "ContigScatterFunction";
+        else
+            return "IntervalScatterFunction";
+    }
+
+    private void writeClass(String baseClass, String packageName, String className, boolean isScatter,
+                            String constructor, List<? extends ArgumentField> argumentFields) throws IOException {
+        String content = getContent(CLASS_TEMPLATE, baseClass, packageName, className, constructor, isScatter, "", argumentFields);
         writeFile(packageName + "." + className, content);
     }
 
     private void writeFilter(String packageName, String className, List<? extends ArgumentField> argumentFields) throws IOException {
         String content = getContent(TRAIT_TEMPLATE, "org.broadinstitute.sting.queue.function.CommandLineFunction",
-                packageName, className, "", String.format(" + \" -read_filter %s\"", className), argumentFields);
+                packageName, className, "", false, String.format(" + \" -read_filter %s\"", className), argumentFields);
         writeFile(packageName + "." + className, content);
     }
 
@@ -172,12 +187,12 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
     }
 
     private static String getContent(String scalaTemplate, String baseClass, String packageName, String className,
-                                     String constructor, String commandLinePrefix, List<? extends ArgumentField> argumentFields) {
+                                     String constructor, boolean isScatter,
+                                     String commandLinePrefix, List<? extends ArgumentField> argumentFields) {
         StringBuilder arguments = new StringBuilder();
         StringBuilder commandLine = new StringBuilder(commandLinePrefix);
 
         Set<String> importSet = new HashSet<String>();
-        boolean isScatter = false;
         boolean isGather = false;
         List<String> freezeFields = new ArrayList<String>();
         for(ArgumentField argumentField: argumentFields) {
@@ -186,13 +201,11 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
             importSet.addAll(argumentField.getImportStatements());
             freezeFields.add(argumentField.getFreezeFields());
 
-            isScatter |= argumentField.isScatter();
             isGather |= argumentField.isGather();
         }
 
         if (isScatter) {
             importSet.add("import org.broadinstitute.sting.queue.function.scattergather.ScatterGatherableFunction");
-            importSet.add("import org.broadinstitute.sting.queue.function.scattergather.Scatter");
             baseClass += " with ScatterGatherableFunction";
         }
         if (isGather)
@@ -210,8 +223,10 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
             freezeFieldOverride.append(String.format("}%n%n"));
         }
 
+        String importText = sortedImports.size() == 0 ? "" : NEWLINE + StringUtils.join(sortedImports, NEWLINE) + NEWLINE;
+
         // see CLASS_TEMPLATE and TRAIT_TEMPLATE below
-        return String.format(scalaTemplate, packageName, StringUtils.join(sortedImports, NEWLINE),
+        return String.format(scalaTemplate, packageName, importText,
                 className, baseClass, constructor, arguments, freezeFieldOverride, commandLine);
     }
     
diff --git a/java/src/org/broadinstitute/sting/queue/function/scattergather/Scatter.java b/java/src/org/broadinstitute/sting/queue/function/scattergather/Scatter.java
deleted file mode 100644
index 471f7fe29..000000000
--- a/java/src/org/broadinstitute/sting/queue/function/scattergather/Scatter.java
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
- * Copyright (c) 2010, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.queue.function.scattergather;
-
-import java.lang.annotation.*;
-
-/**
- * Specifies the class type of the CommandLineFunction to scatter an @Input
- * Written in java because scala doesn't support RetentionPolicy.RUNTIME
- */
-@Documented
-@Inherited
-@Retention(RetentionPolicy.RUNTIME)
-@Target({ElementType.FIELD})
-public @interface Scatter {
-    Class value();
-}
diff --git a/scala/qscript/depristo/manySampleUGPerformance.scala b/scala/qscript/depristo/manySampleUGPerformance.scala
index e265b6961..117763a79 100755
--- a/scala/qscript/depristo/manySampleUGPerformance.scala
+++ b/scala/qscript/depristo/manySampleUGPerformance.scala
@@ -16,7 +16,7 @@ val MERGED_DIR = new File("/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/ma
 trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { 
     this.logging_level = "INFO"; 
     this.jarFile = gatkJarFile;
-    this.intervals = new File(TARGET_INTERVAL);
+    this.intervals :+= new File(TARGET_INTERVAL);
     this.reference_sequence = referenceFile; 
     this.jobQueue = "gsa"; 
     this.et = Option(org.broadinstitute.sting.gatk.phonehome.GATKRunReport.PhoneHomeOption.STANDARD);
diff --git a/scala/qscript/depristo/resequencingSamples1KG.scala b/scala/qscript/depristo/resequencingSamples1KG.scala
index 61a3838a7..24def504f 100644
--- a/scala/qscript/depristo/resequencingSamples1KG.scala
+++ b/scala/qscript/depristo/resequencingSamples1KG.scala
@@ -20,7 +20,7 @@ class ManySampleUGPerformanceTesting extends QScript {
   trait UNIVERSAL_GATK_ARGS extends CommandLineGATK {
     this.logging_level = "INFO";
     this.jarFile = gatkJarFile;
-    this.intervals = new File(TARGET_INTERVAL);
+    this.intervals :+= new File(TARGET_INTERVAL);
     this.reference_sequence = referenceFile;
     this.jobQueue = "gsa";
     this.et = Option(org.broadinstitute.sting.gatk.phonehome.GATKRunReport.PhoneHomeOption.STANDARD);
diff --git a/scala/qscript/examples/ExampleUnifiedGenotyper.scala b/scala/qscript/examples/ExampleUnifiedGenotyper.scala
index daf208359..3397d03a4 100644
--- a/scala/qscript/examples/ExampleUnifiedGenotyper.scala
+++ b/scala/qscript/examples/ExampleUnifiedGenotyper.scala
@@ -41,7 +41,7 @@ class ExampleUnifiedGenotyper extends QScript {
   trait UnifiedGenotyperArguments extends CommandLineGATK {
     this.jarFile = qscript.gatkJar
     this.reference_sequence = qscript.referenceFile
-    this.intervals = qscript.intervals
+    this.intervals :+= qscript.intervals
     // Some() is how you set the value for an scala Option.
     // Set the memory limit to 2 gigabytes on each command.
     this.memoryLimit = Some(2)
diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q
index 38dd24994..bc73c23eb 100755
--- a/scala/qscript/fullCallingPipeline.q
+++ b/scala/qscript/fullCallingPipeline.q
@@ -64,7 +64,7 @@ class fullCallingPipeline extends QScript {
   private var pipeline: Pipeline = _
 
   trait CommandLineGATKArgs extends CommandLineGATK {
-    this.intervals = qscript.pipeline.getProject.getIntervalList
+    this.intervals :+= qscript.pipeline.getProject.getIntervalList
     this.jarFile = qscript.gatkJar
     this.reference_sequence = qscript.pipeline.getProject.getReferenceFile
     this.memoryLimit = Some(4)
@@ -118,10 +118,9 @@ class fullCallingPipeline extends QScript {
       realigner.jobOutputFile = new File(".queue/logs/Cleaning/%s/IndelRealigner.out".format(sampleId))
       realigner.analysisName = "RealignBam_"+sampleId
       realigner.input_file = targetCreator.input_file
-      realigner.intervals = qscript.contigIntervals
+      realigner.intervals :+= qscript.contigIntervals
       realigner.targetIntervals = targetCreator.out
       realigner.scatterCount = contigCount
-      realigner.isIntermediate = true
 
       // may need to explicitly run fix mates
       var fixMates = new PicardBamJarFunction {
@@ -134,7 +133,6 @@ class fullCallingPipeline extends QScript {
         }
 
       // realigner.out = cleaned_bam
-      // realigner.scatterClass = classOf[ContigScatterFunction]
       // realigner.setupGatherFunction = { case (f: BamGatherFunction, _) => f.jarFile = qscript.picardFixMatesJar }
       // realigner.jobQueue = "week"
 
@@ -142,9 +140,8 @@ class fullCallingPipeline extends QScript {
       if (realigner.scatterCount > 1) {
         realigner.out = cleaned_bam
         // While gathering run fix mates.
-        realigner.scatterClass = classOf[ContigScatterFunction]
         realigner.setupScatterFunction = {
-          case (scatter: ScatterFunction, _) =>
+          case scatter: ScatterFunction =>
             scatter.commandDirectory = new File("CleanedBams/IntermediateFiles/%s/ScatterGather".format(sampleId))
             scatter.jobOutputFile = new File(IOUtils.CURRENT_DIR_ABS, ".queue/logs/Cleaning/%s/Scatter.out".format(sampleId))
         }
@@ -167,6 +164,7 @@ class fullCallingPipeline extends QScript {
         }
       } else {
         realigner.out = swapExt("CleanedBams/IntermediateFiles/"+sampleId,bam,"bam","unfixed.cleaned.bam")
+        realigner.isIntermediate = true
 
         // Explicitly run fix mates if the function won't be scattered.
 
@@ -175,7 +173,6 @@ class fullCallingPipeline extends QScript {
         fixMates.unfixed = realigner.out
         fixMates.fixed = cleaned_bam
         fixMates.analysisName = "FixMates_"+sampleId
-        fixMates.isIntermediate = true
         // Add the fix mates explicitly
       }
 
@@ -183,7 +180,6 @@ class fullCallingPipeline extends QScript {
       samtoolsindex.jobOutputFile = new File(".queue/logs/Cleaning/%s/SamtoolsIndex.out".format(sampleId))
       samtoolsindex.bamFile = cleaned_bam
       samtoolsindex.analysisName = "index_cleaned_"+sampleId
-      samtoolsindex.isIntermediate = true
 
       if (!qscript.skip_cleaning) {
         if ( realigner.scatterCount > 1 ) {
@@ -238,7 +234,7 @@ class fullCallingPipeline extends QScript {
 
     snps.scatterCount = qscript.num_snp_scatter_jobs
     snps.setupScatterFunction = {
-      case (scatter: ScatterFunction, _) =>
+      case scatter: ScatterFunction =>
         scatter.commandDirectory = new File("SnpCalls/ScatterGather")
         scatter.jobOutputFile = new File(IOUtils.CURRENT_DIR_ABS, ".queue/logs/SNPCalling/ScatterGather/Scatter.out")
     }
diff --git a/scala/qscript/kshakir/CleanBamFile.scala b/scala/qscript/kshakir/CleanBamFile.scala
deleted file mode 100644
index 7d9e92da1..000000000
--- a/scala/qscript/kshakir/CleanBamFile.scala
+++ /dev/null
@@ -1,196 +0,0 @@
-import org.broadinstitute.sting.queue.extensions.firehose.ImportSingleValueFunction
-import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
-import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction
-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="samtools binary", shortName="samtools")
-  var samtoolsBinary: String = _
-
-  @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")
-  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 = _
-
-  @Argument(doc="firehose import jar", shortName="importJar")
-  var firehoseImportJar: File = _
-
-  @Argument(doc="short job queue", shortName="shortQueue", required=false)
-  var shortJobQueue: String = _
-
-  @Argument(doc="firehose host", shortName="FHHost")
-  var firehoseHost: String = _
-
-  @Argument(doc="firehose port", shortName="FHPort")
-  var firehosePort: Int = _
-
-  @Argument(doc="firehose domain", shortName="FHDomain")
-  var firehoseDomain: String = _
-
-  @Argument(doc="clean bam firehose security token", shortName="FHToken")
-  var firehoseSecurityToken: String = _
-
-  @Argument(doc="clean bam firehose entity type", shortName="bamFHEType")
-  var bamFirehoseEntityType: String = _
-
-  @Argument(doc="clean bam firehose entity id", shortName="bamFHEID")
-  var bamFirehoseEntityID: String = _
-
-  @Argument(doc="clean bam firehose annotation type name", shortName="bamFHAnn")
-  var bamFirehoseAnnotationTypeName: String = _
-
-  trait GATKCommonArgs extends CommandLineGATK {
-    this.jarFile = qscript.gatkJar
-    this.reference_sequence = qscript.referenceFile
-    this.intervals = qscript.intervals
-    this.input_file :+= recalibratedBam
-  }
-
-  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
-
-    var fixedBam: File = null
-
-    if (realigner.scatterCount > 1) {
-      realigner.out = baseFile(".cleaned.bam")
-      // While gathering run fix mates.
-      realigner.setupScatterFunction = {
-        case (scatter: IntervalScatterFunction, _) =>
-          scatter.splitIntervalsScript = indelRealignerScatterScript
-      }
-      realigner.setupGatherFunction = {
-        case (gather: BamGatherFunction, _) =>
-          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
-      }
-
-      fixedBam = realigner.out
-    } else {
-      realigner.out = 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.out
-      fixMates.fixed = baseFile(".cleaned.bam")
-
-      fixedBam = fixMates.fixed
-
-      // Add the fix mates explicitly
-      add(fixMates)
-    }
-
-    val bamIndex = new SamtoolsIndexFunction
-    bamIndex.samtools = samtoolsBinary
-    bamIndex.bamFile = fixedBam
-    bamIndex.bamFileIndex = swapExt(fixedBam, "bam", "bam.bai")
-
-    val importer = new ImportSingleValueFunction {
-      /** Files that this job should wait on before running. */
-      @Input(doc="Explicit job dependencies", required=false)
-      var jobDependencies: List[File] = Nil
-    }
-    importer.jobQueue = shortJobQueue
-    importer.jarFile = firehoseImportJar
-    importer.host = firehoseHost
-    importer.port = firehosePort
-    importer.domain = firehoseDomain
-    importer.securityToken = firehoseSecurityToken
-    importer.entityType = bamFirehoseEntityType
-    importer.entityID = bamFirehoseEntityID
-    importer.annotationTypeName = bamFirehoseAnnotationTypeName
-    importer.importValue = fixedBam
-    importer.jobDependencies :+= bamIndex.bamFileIndex
-
-    add(targetCreator, realigner, bamIndex, importer)
-  }
-}
diff --git a/scala/qscript/kshakir/CleanBamFile.sh b/scala/qscript/kshakir/CleanBamFile.sh
deleted file mode 100755
index 98def9efe..000000000
--- a/scala/qscript/kshakir/CleanBamFile.sh
+++ /dev/null
@@ -1,84 +0,0 @@
-#!/bin/sh
-
-ENTITY_TYPE=$1
-ENTITY_ID=$2
-FIREHOSE_TOKEN=$3
-
-FIREHOSE_WORKSPACE=trunk
-FIREHOSE_HOST=firehose
-FIREHOSE_PORT=8080
-FIREHOSE_DOMAIN=gsa
-CLEAN_BAM_ANNOTATION=clean_bam_file
-DEFAULT_QUEUE=gsa
-SHORT_QUEUE=hour
-FIREHOSE_SOURCE_HOME=/humgen/gsa-firehose/firehose/source
-STING_HOME=$FIREHOSE_SOURCE_HOME/Sting
-CGA_HOME=$FIREHOSE_SOURCE_HOME/CancerGenomeAnalysis
-RUN=-run
-TMP_DIR=/broad/shptmp/$USER
-JOB_QUEUE=gsa
-INTERVAL_COUNT=15
-REALIGNER_COUNT=50
-QUEUE_JAR=$STING_HOME/dist/Queue.jar
-GATK_JAR=$STING_HOME/dist/GenomeAnalysisTK.jar
-FIX_MATES_JAR=/seq/software/picard/1.194/bin/FixMateInformation.jar
-SAMTOOLS=/seq/dirseq/samtools/samtools-0.1.7-5/samtools
-FIREHOSE_IMPORT_JAR=$CGA_HOME/analysis_pipeline/tools/dist/ImportSingleValue.jar
-
-CLEAN_BAM_FILE_SCRIPT=$STING_HOME/scala/qscript/kshakir/CleanBamFile.scala
-FIREHOSE_TEST_HARNESS="python $CGA_HOME/analysis_pipeline/scripts/firehose_test_harness.py"
-SPLIT_BY_CONTIG="python $STING_HOME/python/splitIntervalsByContig.py"
-SPLIT_BY_INTERVALS=$STING_HOME/shell/splitIntervals.sh
-MERGE_TEXT=$STING_HOME/shell/mergeText.sh
-CONVERT_BLACKLIST=$CGA_HOME/analysis_pipeline/genepattern/modules/ConvertDependentsList/convert_dependents_list.sh
-
-# Record the Sting version number.
-svnversion $STING_HOME > stingversion.txt
-# If Sting has been modified, record the differences.
-grep -E '^[0-9]+$' stingversion.txt || svn diff $STING_HOME > stingdiff.txt
-
-# Record the CGA version number.
-svnversion $CGA_HOME > cgaversion.txt
-# If CGA has been modified, record the differences.
-grep -E '^[0-9]+$' cgaversion.txt || svn diff $CGA_HOME > cgadiff.txt
-
-# Try to retrieve the blacklist.  If it fails then set it to "".
-$FIREHOSE_TEST_HARNESS -d $FIREHOSE_DOMAIN -w $FIREHOSE_WORKSPACE -n $ENTITY_ID -t $ENTITY_TYPE 'BLACKLIST="${read_group_blacklist}"' && . firehose-populated-commands.sh || BLACKLIST=""
-
-# Retrieve all the required variables and run the pipeline in Queue.
-$FIREHOSE_TEST_HARNESS -d $FIREHOSE_DOMAIN -w $FIREHOSE_WORKSPACE -n $ENTITY_ID -t $ENTITY_TYPE 'REFERENCE_FILE="${reference_file}";BAM_FILE="${recalibrated_bam_file}";DBSNP_FILE="${dbsnp_file}";INTERVAL_FILE="${interval_list}";DATABASE_ID="${database_id}"' && . firehose-populated-commands.sh && \
-\
-JOB_PREFIX=Q-$ENTITY_ID && \
-\
-java \
--Djava.io.tmpdir="$TMP_DIR" \
--jar "$QUEUE_JAR" \
--S "$CLEAN_BAM_FILE_SCRIPT" \
--bsub -bsubWait -skipUpToDate \
--jobQueue "$JOB_QUEUE" \
--jobPrefix "$JOB_PREFIX" \
--gatk "$GATK_JAR" \
--base "$ENTITY_ID" \
--R "$REFERENCE_FILE" \
--I "$BAM_FILE" \
--D "$DBSNP_FILE" \
--L "$INTERVAL_FILE" \
--RTCSS "$SPLIT_BY_CONTIG" \
--RTCSC "$INTERVAL_COUNT" \
--IRSS "$SPLIT_BY_INTERVALS" \
--IRSC "$REALIGNER_COUNT" \
--MTS "$MERGE_TEXT" \
--fixMates "$FIX_MATES_JAR" \
--samtools "$SAMTOOLS" \
--RGBLS "$CONVERT_BLACKLIST" \
--RGBL "$BLACKLIST" \
--importJar "$FIREHOSE_IMPORT_JAR" \
--shortQueue "$SHORT_QUEUE" \
--FHHost "$FIREHOSE_HOST" \
--FHPort "$FIREHOSE_PORT" \
--FHDomain "$FIREHOSE_DOMAIN" \
--FHToken "$FIREHOSE_TOKEN" \
--bamFHEType "$ENTITY_TYPE" \
--bamFHEID "$DATABASE_ID" \
--bamFHAnn "$CLEAN_BAM_ANNOTATION" \
-$RUN || ( echo Job failed. Check stdout.txt for more info. >&2; exit 1; )
diff --git a/scala/qscript/recalibrate.scala b/scala/qscript/recalibrate.scala
index 25c6b2422..6d9464f4a 100755
--- a/scala/qscript/recalibrate.scala
+++ b/scala/qscript/recalibrate.scala
@@ -39,7 +39,7 @@ def script = {
           add(new CountCovariates(bamIn, recalData) { useOriginalQualities = true } )
       val tableRecal = new TableRecalibrate(bamIn, recalData, recalBam) { useOriginalQualities = true }
       if ( scatter ) {
-          tableRecal.intervals = new File("/humgen/gsa-hpprojects/GATK/data/chromosomes.hg18.interval_list")
+          tableRecal.intervals :+= new File("/humgen/gsa-hpprojects/GATK/data/chromosomes.hg18.interval_list")
 	  //tableRecal.scatterClass = classOf[ContigScatterFunction]
 	  tableRecal.setupGatherFunction = { case (f: PicardBamJarFunction, _) => f.jarFile = picardMergeSamFilesJar; f.memoryLimit = Some(4) }
       	  tableRecal.scatterCount = 25
diff --git a/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala b/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
index ac8885f5a..c86a40f52 100755
--- a/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
+++ b/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
@@ -26,8 +26,8 @@ class QCommandLine extends CommandLineProgram with Logging {
   @Argument(fullName="expanded_dot_graph", shortName="expandedDot", doc="Outputs the queue graph of scatter gather to a .dot file.  Otherwise overwrites the dot_graph", required=false)
   private var expandedDotFile: File = _
 
-  @Argument(fullName="start_clean", shortName="clean", doc="Runs all command line functions even if the outputs were previously output successfully.", required=false)
-  private var startClean = false
+  @Argument(fullName="start_from_scratch", shortName="startFromScratch", doc="Runs all command line functions even if the outputs were previously output successfully.", required=false)
+  private var startFromScratch = false
 
   @Argument(fullName="for_reals", shortName="forReals", doc="Run QScripts", required=false) @Hidden
   private var runScripts = false
@@ -38,12 +38,15 @@ class QCommandLine extends CommandLineProgram with Logging {
   @ArgumentCollection
   private val qSettings = new QSettings
 
-  @Argument(fullName="statusEmailFrom", shortName="statusFrom", doc="Email address to send emails from upon completion or on error.", required=false)
+  @Argument(fullName="status_email_from", shortName="statusFrom", doc="Email address to send emails from upon completion or on error.", required=false)
   private var statusEmailFrom: String = System.getProperty("user.name") + "@" + SystemUtils.domainName
 
-  @Argument(fullName="statusEmailTo", shortName="statusTo", doc="Email address to send emails to upon completion or on error.", required=false)
+  @Argument(fullName="status_email_to", shortName="statusTo", doc="Email address to send emails to upon completion or on error.", required=false)
   private var statusEmailTo: List[String] = Nil
 
+  @Argument(fullName="delete_intermediate_outputs", shortName="deleteIntermediates", doc="After a successful run delete the outputs of any Function marked as intermediate.", required=false)
+  private var deleteIntermediates = false
+
   /**
    * Takes the QScripts passed in, runs their script() methods, retrieves their generated
    * functions, and then builds and runs a QGraph based on the dependencies.
@@ -53,13 +56,14 @@ class QCommandLine extends CommandLineProgram with Logging {
     val qGraph = new QGraph
     qGraph.dryRun = !(run || runScripts)
     qGraph.bsubAllJobs = bsubAllJobs
-    qGraph.startClean = startClean
+    qGraph.startFromScratch = startFromScratch
     qGraph.dotFile = dotFile
     qGraph.expandedDotFile = expandedDotFile
     qGraph.qSettings = qSettings
     qGraph.debugMode = debugMode == true
     qGraph.statusEmailFrom = statusEmailFrom
     qGraph.statusEmailTo = statusEmailTo
+    qGraph.deleteIntermediates = deleteIntermediates
 
     val scripts = qScriptManager.createScripts()
     for (script <- scripts) {
diff --git a/scala/src/org/broadinstitute/sting/queue/QScript.scala b/scala/src/org/broadinstitute/sting/queue/QScript.scala
index 363e56831..3736abdaa 100755
--- a/scala/src/org/broadinstitute/sting/queue/QScript.scala
+++ b/scala/src/org/broadinstitute/sting/queue/QScript.scala
@@ -16,7 +16,6 @@ trait QScript extends Logging {
   type CommandLineFunction = org.broadinstitute.sting.queue.function.CommandLineFunction
   type InProcessFunction = org.broadinstitute.sting.queue.function.InProcessFunction
   type ScatterGatherableFunction = org.broadinstitute.sting.queue.function.scattergather.ScatterGatherableFunction
-  type Scatter = org.broadinstitute.sting.queue.function.scattergather.Scatter
   type Gather = org.broadinstitute.sting.queue.function.scattergather.Gather
   type SimpleTextGatherFunction = org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction
 
diff --git a/scala/src/org/broadinstitute/sting/queue/engine/FunctionEdge.scala b/scala/src/org/broadinstitute/sting/queue/engine/FunctionEdge.scala
index 84d9b7e2b..b3bb52d98 100644
--- a/scala/src/org/broadinstitute/sting/queue/engine/FunctionEdge.scala
+++ b/scala/src/org/broadinstitute/sting/queue/engine/FunctionEdge.scala
@@ -33,10 +33,10 @@ class FunctionEdge(var function: QFunction) extends QEdge {
     currentStatus = RunnerStatus.SKIPPED
   }
 
-  def resetToPending() = {
+  def resetToPending(cleanOutputs: Boolean) = {
     currentStatus = RunnerStatus.PENDING
-    function.doneOutputs.foreach(_.delete())
-    function.failOutputs.foreach(_.delete())
+    if (cleanOutputs)
+      function.deleteOutputs()
   }
 
   def inputs = function.inputs
diff --git a/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala b/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
index 7aa0920bb..1d7dda969 100755
--- a/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
+++ b/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
@@ -21,11 +21,12 @@ import org.apache.commons.lang.StringUtils
 class QGraph extends Logging {
   var dryRun = true
   var bsubAllJobs = false
-  var startClean = false
+  var startFromScratch = false
   var dotFile: File = _
   var expandedDotFile: File = _
   var qSettings: QSettings = _
   var debugMode = false
+  var deleteIntermediates = false
   var statusEmailFrom: String = _
   var statusEmailTo: List[String] = _
 
@@ -127,6 +128,7 @@ class QGraph extends Logging {
     // build up the full DAG with scatter-gather jobs
     fillGraph
     logger.info("Checking pipeline status.")
+    updateGraphStatus(false)
     logStatus
   }
 
@@ -241,24 +243,18 @@ class QGraph extends Logging {
    * Dry-runs the jobs by traversing the graph.
    */
   private def dryRunJobs() = {
-    traverseFunctions(edge => {
-      edge.function match {
-        case qFunction => {
-          if (logger.isDebugEnabled) {
-            logger.debug(qFunction.commandDirectory + " > " + qFunction.description)
-          } else {
-            logger.info(qFunction.description)
-          }
-          logger.info("Output written to " + qFunction.jobOutputFile)
-          if (qFunction.jobErrorFile != null) {
-            logger.info("Errors written to " + qFunction.jobErrorFile)
-          } else {
-            if (logger.isDebugEnabled)
-              logger.info("Errors also written to " + qFunction.jobOutputFile)
-          }
-        }
-      }
-    })
+    updateGraphStatus(false)
+    traverseFunctions(edge => logEdge(edge))
+  }
+
+  private def logEdge(edge: FunctionEdge) = {
+    logger.info("-------")
+    logger.info(StringUtils.capitalize(edge.status.toString) + ": " + edge.function.description)
+    if (logger.isDebugEnabled)
+      logger.debug(edge.function.commandDirectory + " > " + edge.function.description)
+    logger.info("Log: " + edge.function.jobOutputFile.getAbsolutePath)
+    if (edge.function.jobErrorFile != null)
+      logger.info("Error: " + edge.function.jobErrorFile.getAbsolutePath)
   }
 
   /**
@@ -266,12 +262,11 @@ class QGraph extends Logging {
    */
   private def runJobs() = {
     try {
-      traverseFunctions(edge => {
-        if (startClean)
-          edge.resetToPending()
-        else
-          checkDone(edge)
-      })
+      if (startFromScratch) {
+        logger.info("Removing outputs from previous runs.")
+        foreachFunction(_.resetToPending(true))
+      } else
+        updateGraphStatus(true)
 
       var readyJobs = getReadyJobs
       var runningJobs = Set.empty[FunctionEdge]
@@ -303,6 +298,8 @@ class QGraph extends Logging {
           Thread.sleep(30000L)
         readyJobs = getReadyJobs
       }
+
+      deleteIntermediateOutputs()
     } catch {
       case e =>
         logger.error("Uncaught error running jobs.", e)
@@ -312,13 +309,22 @@ class QGraph extends Logging {
     }
   }
 
+  /**
+   * Updates the status of edges in the graph.
+   * @param cleanOutputs If true will delete outputs when setting edges to pending.
+   */
+  private def updateGraphStatus(cleanOutputs: Boolean) = {
+    traverseFunctions(edge => checkDone(edge, cleanOutputs))
+  }
+
   /**
    * Checks if an edge is done or if it's an intermediate edge if it can be skipped.
    * This function may modify previous edges if it discovers that the edge passed in
    * is dependent jobs that were previously marked as skipped.
    * @param edge Edge to check to see if it's done or can be skipped.
+   * @param cleanOutputs If true will delete outputs when setting edges to pending.
    */
-  private def checkDone(edge: FunctionEdge) = {
+  private def checkDone(edge: FunctionEdge, cleanOutputs: Boolean) = {
     if (edge.function.isIntermediate) {
       // By default we do not need to run intermediate edges.
       // Mark any intermediate edges as skipped, if they're not already done.
@@ -329,8 +335,8 @@ class QGraph extends Logging {
       val isDone = edge.status == RunnerStatus.DONE &&
               previous.forall(edge => edge.status == RunnerStatus.DONE || edge.status == RunnerStatus.SKIPPED)
       if (!isDone) {
-        edge.resetToPending()
-        resetPreviousSkipped(edge, previous)
+        edge.resetToPending(cleanOutputs)
+        resetPreviousSkipped(edge, previous, cleanOutputs)
       }
     }
   }
@@ -341,11 +347,12 @@ class QGraph extends Logging {
    * to pending.
    * @param edge Dependent edge.
    * @param previous Previous edges that provide inputs to edge.
+   * @param cleanOutputs If true will clean up the output files when resetting skipped jobs to pending.
    */
-  private def resetPreviousSkipped(edge: FunctionEdge, previous: List[FunctionEdge]): Unit = {
+  private def resetPreviousSkipped(edge: FunctionEdge, previous: List[FunctionEdge], cleanOutputs: Boolean): Unit = {
     for (previousEdge <- previous.filter(_.status == RunnerStatus.SKIPPED)) {
-      previousEdge.resetToPending()
-      resetPreviousSkipped(previousEdge, this.previousFunctions(previousEdge))
+      previousEdge.resetToPending(cleanOutputs)
+      resetPreviousSkipped(previousEdge, this.previousFunctions(previousEdge), cleanOutputs)
     }
   }
 
@@ -468,7 +475,7 @@ class QGraph extends Logging {
     foreachFunction(edge => {
       val name = edge.function.analysisName
       if (name != null) {
-        updateStatus(statuses.find(_.analysisName == name) match {
+        updateAnalysisStatus(statuses.find(_.analysisName == name) match {
           case Some(status) => status
           case None =>
             val status = new AnalysisStatus(name)
@@ -484,11 +491,13 @@ class QGraph extends Logging {
       val sgDone = status.scatter.done + status.gather.done
       val sgFailed = status.scatter.failed + status.gather.failed
       val sgSkipped = status.scatter.skipped + status.gather.skipped
+      val gatherTotal = status.gather.total
+      val gatherDone = status.gather.done
       if (sgTotal > 0) {
         var sgStatus = RunnerStatus.PENDING
         if (sgFailed > 0)
           sgStatus = RunnerStatus.FAILED
-        else if (sgDone == sgTotal)
+        else if (gatherDone == gatherTotal)
           sgStatus = RunnerStatus.DONE
         else if (sgDone + sgSkipped == sgTotal)
           sgStatus = RunnerStatus.SKIPPED
@@ -510,7 +519,7 @@ class QGraph extends Logging {
   /**
    * Updates a status map with scatter/gather status information (e.g. counts)
    */
-  private def updateStatus(stats: AnalysisStatus, edge: FunctionEdge) = {
+  private def updateAnalysisStatus(stats: AnalysisStatus, edge: FunctionEdge) = {
     if (edge.function.isInstanceOf[GatherFunction]) {
       updateSGStatus(stats.gather, edge)
     } else if (edge.function.isInstanceOf[CloneFunction]) {
@@ -671,7 +680,19 @@ class QGraph extends Logging {
       }
     })
     iterator.foreach(_ => {})
-  }  
+  }
+
+  private def deleteIntermediateOutputs() = {
+    if (this.deleteIntermediates && !hasFailed) {
+      logger.info("Deleting intermediate files.")
+      traverseFunctions(edge => {
+        if (edge.function.isIntermediate) {
+          logger.debug("Deleting intermediates:" + edge.function.description)
+          edge.function.deleteOutputs()
+        }
+      })
+    }
+  }
 
   /**
    * Outputs the graph to a .dot file.
@@ -705,13 +726,8 @@ class QGraph extends Logging {
 
   def logFailed = {
     foreachFunction(edge => {
-      if (edge.status == RunnerStatus.FAILED) {
-        logger.error("-----")
-        logger.error("Failed: " + edge.function.description)
-        logger.error("Log: " + edge.function.jobOutputFile.getAbsolutePath)
-        if (edge.function.jobErrorFile != null)
-          logger.error("Error: " + edge.function.jobErrorFile.getAbsolutePath)
-      }
+      if (edge.status == RunnerStatus.FAILED)
+        logEdge(edge)
     })
   }
 
diff --git a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala
index ff8cc4c7c..2fb327e3f 100644
--- a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala
@@ -1,8 +1,6 @@
 package org.broadinstitute.sting.queue.extensions.gatk
 
-import org.broadinstitute.sting.queue.function.InProcessFunction
 import org.broadinstitute.sting.commandline.ArgumentSource
-import org.broadinstitute.sting.queue.function.scattergather.{ScatterGatherableFunction, ScatterFunction}
 import org.broadinstitute.sting.utils.interval.IntervalUtils
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceDataSource
 import java.io.File
@@ -10,6 +8,10 @@ import net.sf.picard.util.IntervalList
 import net.sf.samtools.SAMFileHeader
 import collection.JavaConversions._
 import org.broadinstitute.sting.utils.{GenomeLoc, GenomeLocSortedSet, GenomeLocParser}
+import org.broadinstitute.sting.queue.util.IOUtils
+import org.broadinstitute.sting.queue.function.scattergather.{CloneFunction, ScatterGatherableFunction, ScatterFunction}
+import org.broadinstitute.sting.queue.function.{QFunction, InProcessFunction}
+import org.broadinstitute.sting.queue.QException
 
 /**
  * An interval scatter function.
@@ -18,19 +20,45 @@ class IntervalScatterFunction extends ScatterFunction with InProcessFunction {
   var splitByContig = false
 
   private var referenceSequence: File = _
+  private var intervalField: ArgumentSource = _
   private var intervals: List[String] = Nil
 
-  override def setOriginalFunction(originalFunction: ScatterGatherableFunction, scatterField: ArgumentSource) = {
+  def isScatterGatherable(originalFunction: ScatterGatherableFunction) = {
+    if (originalFunction.isInstanceOf[CommandLineGATK]) {
+      val gatk = originalFunction.asInstanceOf[CommandLineGATK]
+      gatk.reference_sequence != null
+    } else false
+  }
+
+  def setScatterGatherable(originalFunction: ScatterGatherableFunction) = {
     val gatk = originalFunction.asInstanceOf[CommandLineGATK]
-    referenceSequence = gatk.reference_sequence
-    intervals = gatk.intervalsString
-    if (gatk.intervals != null)
-      intervals ::= gatk.intervals.toString
+    this.referenceSequence = gatk.reference_sequence
+    this.intervals ++= gatk.intervalsString
+    this.intervals ++= gatk.intervals.map(_.toString)
+    this.intervalField = QFunction.findField(originalFunction.getClass, "intervals")
+  }
+
+  def initCloneInputs(cloneFunction: CloneFunction, index: Int) = {
+    cloneFunction.setFieldValue(this.intervalField, List(new File("scatter.intervals")))
+  }
+
+  def bindCloneInputs(cloneFunction: CloneFunction, index: Int) = {
+    val scatterPart = cloneFunction.getFieldValue(this.intervalField)
+            .asInstanceOf[List[File]]
+            .map(file => IOUtils.subDir(cloneFunction.commandDirectory, file))
+    cloneFunction.setFieldValue(this.intervalField, scatterPart)
+    this.scatterParts ++= scatterPart
   }
 
   def run() = {
-    val referenceSource = new ReferenceDataSource(referenceSequence)
-    GenomeLocParser.setupRefContigOrdering(referenceSource.getReference);
+    IntervalScatterFunction.scatter(this.intervals, this.scatterParts, this.referenceSequence, this.splitByContig)
+  }
+}
+
+object IntervalScatterFunction {
+  def scatter(intervals: List[String], scatterParts: List[File], reference: File, splitByContig: Boolean) = {
+    val referenceSource = new ReferenceDataSource(reference)
+    GenomeLocParser.setupRefContigOrdering(referenceSource.getReference)
     val locs = {
       // TODO: Abstract genome analysis engine has richer logic for parsing.  We need to use it!
       if (intervals.size == 0) {
@@ -47,6 +75,9 @@ class IntervalScatterFunction extends ScatterFunction with InProcessFunction {
     var fileIndex = -1
     var locIndex = 0
 
+    if (locs == null || locs.size == 0)
+      throw new QException("Locs produced an empty interval list: " + intervals.mkString(", "))
+
     if (splitByContig) {
       var contig: String = null
       for (loc <- locs) {
@@ -54,29 +85,48 @@ class IntervalScatterFunction extends ScatterFunction with InProcessFunction {
           if (fileIndex >= 0)
             intervalList.write(scatterParts(fileIndex))
           fileIndex += 1
+          contig = loc.getContig
           intervalList = new IntervalList(fileHeader)
         }
         locIndex += 1
         intervalList.add(toInterval(loc, locIndex))
       }
       intervalList.write(scatterParts(fileIndex))
+      if ((fileIndex + 1) != scatterParts.size)
+        throw new QException("Only able to write contigs into %d of %d files.".format(fileIndex + 1, scatterParts.size))
     } else {
-      var locsPerFile = locs.size / this.scatterParts.size
-      if (locs.size % this.scatterParts.size != 0) locsPerFile += 1
+      var locsPerFile = locs.size / scatterParts.size
+      val locRemainder = locs.size % scatterParts.size
+
+      // At the start, put an extra loc per file
+      locsPerFile += 1
+      var locsLeftFile = 0
+
       for (loc <- locs) {
-        if (locIndex % locsPerFile == 0) {
+        if (locsLeftFile == 0) {
           if (fileIndex >= 0)
             intervalList.write(scatterParts(fileIndex))
+
           fileIndex += 1
           intervalList = new IntervalList(fileHeader)
+
+          // When we have put enough locs into each file,
+          // reduce the number of locs per file back
+          // to the original calculated value.
+          if (fileIndex == locRemainder)
+            locsPerFile -= 1
+          locsLeftFile = locsPerFile
         }
+        locsLeftFile -= 1
         locIndex += 1
         intervalList.add(toInterval(loc, locIndex))
       }
       intervalList.write(scatterParts(fileIndex))
+      if ((fileIndex + 1) != scatterParts.size)
+        throw new QException("Only able to write intervals into %d of %d files.".format(fileIndex + 1, scatterParts.size))
     }
   }
 
   private def toInterval(loc: GenomeLoc, locIndex: Int) =
-    new net.sf.picard.util.Interval(loc.getContig, loc.getStart.toInt, loc.getStop.toInt, true, "interval_" + locIndex)
+    new net.sf.picard.util.Interval(loc.getContig, loc.getStart.toInt, loc.getStop.toInt, false, "interval_" + locIndex)
 }
diff --git a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala
new file mode 100644
index 000000000..c271d5eca
--- /dev/null
+++ b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala
@@ -0,0 +1,46 @@
+package org.broadinstitute.sting.queue.extensions.gatk
+
+import org.broadinstitute.sting.queue.function.InProcessFunction
+import org.broadinstitute.sting.queue.QException
+import org.broadinstitute.sting.queue.function.scattergather.GatherFunction
+import java.io.{FileReader, PrintWriter}
+import org.apache.commons.io.{LineIterator, IOUtils, FileUtils}
+
+/**
+ * Merges a vcf text file.
+ */
+class VcfGatherFunction extends GatherFunction with InProcessFunction {
+  def run() = {
+    if (gatherParts.size < 1) {
+      throw new QException("No files to gather to output: " + originalOutput)
+    } else {
+      val writer = new PrintWriter(originalOutput)
+      try {
+        var reader = new FileReader(gatherParts(0))
+        try {
+          IOUtils.copy(reader, writer)
+        } finally {
+          IOUtils.closeQuietly(reader)
+        }
+
+        for (file <- gatherParts.tail) {
+          var inHeaders = true
+          val itor = FileUtils.lineIterator(file)
+          try {
+            while (itor.hasNext) {
+              val nextLine = itor.nextLine
+              if (inHeaders && nextLine(0) != '#')
+                inHeaders = false
+              if (!inHeaders)
+                writer.println(nextLine)
+            }
+          } finally {
+            LineIterator.closeQuietly(itor)
+          }
+        }
+      } finally {
+        IOUtils.closeQuietly(writer)
+      }
+    }
+  }
+}
\ No newline at end of file
diff --git a/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
index 695fe629b..4888749e9 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala
@@ -152,6 +152,15 @@ trait QFunction {
     dirs
   }
 
+  /**
+   * Deletes the output files and all the status files for this function.
+   */
+  def deleteOutputs() = {
+    outputs.foreach(_.delete())
+    doneOutputs.foreach(_.delete())
+    failOutputs.foreach(_.delete())
+  }
+
   /**
    * Creates the output directories for this function if it doesn't exist.
    */
@@ -416,6 +425,19 @@ object QFunction {
    */
   private var classFieldsMap = Map.empty[Class[_], ClassFields]
 
+  /**
+   * Returns the field on clazz.
+   * @param clazz Class to search.
+   * @param name Name of the field to return.
+   * @return Argument source for the field.
+   */
+  def findField(clazz: Class[_], name: String) = {
+    classFields(clazz).functionFields.find(_.field.getName == name) match {
+      case Some(source) => source
+      case None => throw new QException("Could not find a field on class %s with name %s".format(clazz, name))
+    }
+  }
+
   /**
    * Returns the fields for a class.
    * @param clazz Class to retrieve fields for.
diff --git a/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala
index 16748bf6a..b7451f69e 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala
@@ -3,6 +3,7 @@ package org.broadinstitute.sting.queue.function.scattergather
 import org.broadinstitute.sting.queue.function.CommandLineFunction
 import org.broadinstitute.sting.commandline.ArgumentSource
 import java.io.File
+import org.broadinstitute.sting.queue.QException
 
 /**
  * Shadow clones another command line function.
@@ -61,7 +62,7 @@ class CloneFunction extends CommandLineFunction {
     }
   }
 
-  override def setFieldValue(source: ArgumentSource, value: Any) = {
+  override def setFieldValue(source: ArgumentSource, value: Any): Unit = {
     source.field.getName match {
       case "jobOutputFile" => jobOutputFile = value.asInstanceOf[File]
       case "jobErrorFile" => jobErrorFile = value.asInstanceOf[File]
diff --git a/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala
index e9649adc8..8bf5d7082 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.queue.function.scattergather
 
 import java.io.File
-import org.broadinstitute.sting.commandline.{ArgumentSource, Input, Output}
+import org.broadinstitute.sting.commandline.{Input, Output}
 import org.broadinstitute.sting.queue.function.QFunction
 
 /**
@@ -13,19 +13,4 @@ trait GatherFunction extends QFunction {
 
   @Output(doc="The original output of the scattered function")
   var originalOutput: File = _
-
-  /**
-   * Sets the original function used to create this scatter function.
-   * @param originalFunction The ScatterGatherableFunction.
-   * @param gatherField The field being gathered.
-   */
-  def setOriginalFunction(originalFunction: ScatterGatherableFunction, gatherField: ArgumentSource) = {}
-
-  /**
-   * Sets the clone function creating one of the inputs for this gather function.
-   * @param cloneFunction The clone wrapper for the original ScatterGatherableFunction.
-   * @param index The one based index (from 1..scatterCount inclusive) of the scatter piece.
-   * @param gatherField The field to be gathered.
-   */
-  def setCloneFunction(cloneFunction: CloneFunction, index: Int, gatherField: ArgumentSource) = {}
 }
diff --git a/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala
index bf6d026b5..86e9ab921 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala
@@ -1,31 +1,47 @@
 package org.broadinstitute.sting.queue.function.scattergather
 
 import java.io.File
-import org.broadinstitute.sting.commandline.{ArgumentSource, Input, Output}
+import org.broadinstitute.sting.commandline.{Input, Output}
 import org.broadinstitute.sting.queue.function.QFunction
 
 /**
- * Base class for Scatter command line functions.
+ * Base class for Scatter functions.
  */
 trait ScatterFunction extends QFunction {
-  @Input(doc="Original input to scatter")
-  var originalInput: File = _
+  @Input(doc="Original inputs to scatter")
+  var originalInputs: Set[File] = _
 
-  @Output(doc="Scattered parts of the original input, one per temp directory")
+  @Output(doc="Scattered parts of the original inputs, one set per temp directory")
   var scatterParts: List[File] = Nil
 
   /**
-   * Sets the original function used to create this scatter function.
-   * @param originalFunction The ScatterGatherableFunction.
-   * @param scatterField The field being scattered.
+   * Returns true if the scatter function can scatter this original function.
+   * @param originalFunction The original function to check.
+   * @return true if the scatter function can scatter this original function.
    */
-  def setOriginalFunction(originalFunction: ScatterGatherableFunction, scatterField: ArgumentSource) = {}
+  def isScatterGatherable(originalFunction: ScatterGatherableFunction): Boolean
 
   /**
-   * Sets the clone function using one of the outputs of this scatter function.
-   * @param cloneFunction The clone wrapper for the original ScatterGatherableFunction.
-   * @param index The one based index (from 1..scatterCount inclusive) of the scatter piece.
-   * @param scatterField The field being scattered.
+   * Sets the original ScatterGatherableFunction to be scattered.
+   * @param originalFunction The original function to with inputs bind to this scatter function.
    */
-  def setCloneFunction(cloneFunction: CloneFunction, index: Int, scatterField: ArgumentSource) = {}
+  def setScatterGatherable(originalFunction: ScatterGatherableFunction)
+
+  /**
+   * Initializes the input fields for the clone function.
+   * The input values should be set to their defaults
+   * and may be changed by the user.
+   * @param cloneFunction CloneFunction to initialize.
+   * @param index The one based scatter index.
+   */
+  def initCloneInputs(cloneFunction: CloneFunction, index: Int)
+
+  /**
+   * Binds the input fields for the clone function to this scatter function.
+   * The input values should be set to their absolute values and added
+   * to scatter parts.
+   * @param cloneFunction CloneFunction to bind.
+   * @param index The one based scatter index.
+   */
+  def bindCloneInputs(cloneFunction: CloneFunction, index: Int)
 }
diff --git a/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
index 2aebfef3d..4bc270436 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
@@ -4,6 +4,7 @@ import java.io.File
 import org.broadinstitute.sting.queue.util._
 import org.broadinstitute.sting.commandline.ArgumentSource
 import org.broadinstitute.sting.queue.function.{QFunction, CommandLineFunction}
+import org.broadinstitute.sting.queue.QException
 
 /**
  * A function that can be run faster by splitting it up into pieces and then joining together the results.
@@ -29,9 +30,8 @@ trait ScatterGatherableFunction extends CommandLineFunction {
   /**
    * Allows external modification of the ScatterFunction that will create the scatter pieces in the temporary directories.
    * @param scatterFunction The function that will create the scatter pieces in the temporary directories.
-   * @param scatterField The input field being scattered.
    */
-  var setupScatterFunction: PartialFunction[(ScatterFunction, ArgumentSource), Unit] = _
+  var setupScatterFunction: PartialFunction[ScatterFunction, Unit] = _
 
   /**
    * Allows external modification of the GatherFunction that will collect the gather pieces in the temporary directories.
@@ -50,10 +50,10 @@ trait ScatterGatherableFunction extends CommandLineFunction {
   /**
    * Returns true if the function is ready to be scatter / gathered.
    * The base implementation checks if the scatter count is greater than one,
-   * and that the scatter field has a value.
+   * and that the scatter function can scatter this instance.
    * @return true if the function is ready to be scatter / gathered.
    */
-  def scatterGatherable = this.scatterCount > 1 && hasFieldValue(this.scatterField)
+  def scatterGatherable = this.scatterCount > 1 && scatterFunction.isScatterGatherable(this)
 
   /**
    * Returns a list of scatter / gather and clones of this function
@@ -68,17 +68,15 @@ trait ScatterGatherableFunction extends CommandLineFunction {
     val inputFieldsWithValues = this.inputFields.filter(hasFieldValue(_))
     // Only gather up fields that will have a value
     val outputFieldsWithValues = this.outputFields.filter(hasFieldValue(_))
-    // The field containing the file to split
-    val originalInput = getFieldFile(scatterField)
 
     // Create the scatter function based on @Scatter
-    val scatterFunction = this.newScatterFunction(this.scatterField)
     syncFunction(scatterFunction)
     scatterFunction.addOrder = this.addOrder :+ 1
-    scatterFunction.commandDirectory = this.scatterGatherTempDir("scatter-" + scatterField.field.getName)
-    scatterFunction.originalInput = originalInput
-    scatterFunction.setOriginalFunction(this, scatterField)
-    initScatterFunction(scatterFunction, this.scatterField)
+    scatterFunction.commandDirectory = this.scatterGatherTempDir("scatter")
+    scatterFunction.originalInputs = this.inputs
+    scatterFunction.isIntermediate = true
+    scatterFunction.setScatterGatherable(this)
+    initScatterFunction(scatterFunction)
     functions :+= scatterFunction
 
     // Create the gather functions for each output field
@@ -92,7 +90,7 @@ trait ScatterGatherableFunction extends CommandLineFunction {
       gatherFunction.addOrder = this.addOrder :+ gatherAddOrder
       gatherFunction.commandDirectory = this.scatterGatherTempDir("gather-" + gatherField.field.getName)
       gatherFunction.originalOutput = this.getFieldFile(gatherField)
-      gatherFunction.setOriginalFunction(this, gatherField)
+      gatherFunction.isIntermediate = this.isIntermediate
       initGatherFunction(gatherFunction, gatherField)
       functions :+= gatherFunction
       gatherFunctions += gatherField -> gatherFunction
@@ -110,11 +108,11 @@ trait ScatterGatherableFunction extends CommandLineFunction {
       cloneFunction.index = i
       cloneFunction.addOrder = this.addOrder :+ (i+1)
       cloneFunction.memoryLimit = this.memoryLimit
+      cloneFunction.isIntermediate = true
 
       // Setup the fields on the clone function, outputting each as a relative file in the sg directory.
       cloneFunction.commandDirectory = this.scatterGatherTempDir("temp-"+i)
-      var scatterPart = new File(originalInput.getName)
-      cloneFunction.setFieldValue(scatterField, scatterPart)
+      scatterFunction.initCloneInputs(cloneFunction, i)
       for (gatherField <- outputFieldsWithValues) {
         val gatherPart = new File(gatherOutputs(gatherField).getName)
         cloneFunction.setFieldValue(gatherField, gatherPart)
@@ -124,9 +122,7 @@ trait ScatterGatherableFunction extends CommandLineFunction {
       initCloneFunction(cloneFunction, i)
 
       // Get absolute paths to the files and bind the sg functions to the clone function via the absolute paths.
-      scatterPart = IOUtils.subDir(cloneFunction.commandDirectory, cloneFunction.getFieldFile(scatterField))
-      cloneFunction.setFieldValue(scatterField, scatterPart)
-      scatterFunction.scatterParts :+= scatterPart
+      scatterFunction.bindCloneInputs(cloneFunction, i)
       for (gatherField <- outputFieldsWithValues) {
         val gatherPart = IOUtils.subDir(cloneFunction.commandDirectory, cloneFunction.getFieldFile(gatherField))
         cloneFunction.setFieldValue(gatherField, gatherPart)
@@ -137,7 +133,7 @@ trait ScatterGatherableFunction extends CommandLineFunction {
     }
     functions ++= cloneFunctions
 
-    // Return all the various functions we created
+    // Return all the various created functions.
     functions
   }
 
@@ -155,34 +151,24 @@ trait ScatterGatherableFunction extends CommandLineFunction {
   }
 
   /**
-   * Retrieves the scatter field from the first field that has the annotation @Scatter.
+   * Creates a new ScatterFunction.
+   * @return A ScatterFunction instantiated scatterClass
    */
-  protected lazy val scatterField =
-    this.inputFields.find(field => ReflectionUtils.hasAnnotation(field.field, classOf[Scatter])).get
-
-  /**
-   * Creates a new ScatterFunction for the scatterField.
-   * @param scatterField Field that defined @Scatter.
-   * @return A ScatterFunction instantiated from @Scatter or scatterClass if scatterClass was set on this ScatterGatherableFunction.
-   */
-  protected def newScatterFunction(scatterField: ArgumentSource): ScatterFunction = {
-    var scatterClass = this.scatterClass
-    if (scatterClass == null)
-      scatterClass = ReflectionUtils.getAnnotation(scatterField.field, classOf[Scatter])
-              .value.asSubclass(classOf[ScatterFunction])
-    scatterClass.newInstance.asInstanceOf[ScatterFunction]
+  protected def newScatterFunction(): ScatterFunction = {
+    if (this.scatterClass == null)
+      throw new QException("scatterClass is null.")
+    this.scatterClass.newInstance.asInstanceOf[ScatterFunction]
   }
 
   /**
    * Initializes the ScatterFunction created by newScatterFunction() that will create the scatter pieces in the temporary directories.
    * Calls setupScatterFunction with scatterFunction.
    * @param scatterFunction The function that will create the scatter pieces in the temporary directories.
-   * @param scatterField The input field being scattered.
    */
-  protected def initScatterFunction(scatterFunction: ScatterFunction, scatterField: ArgumentSource) = {
+  protected def initScatterFunction(scatterFunction: ScatterFunction) = {
     if (this.setupScatterFunction != null)
-      if (this.setupScatterFunction.isDefinedAt(scatterFunction, scatterField))
-        this.setupScatterFunction(scatterFunction, scatterField)
+      if (this.setupScatterFunction.isDefinedAt(scatterFunction))
+        this.setupScatterFunction(scatterFunction)
   }
 
   /**
@@ -236,7 +222,6 @@ trait ScatterGatherableFunction extends CommandLineFunction {
    * @param newFunction newly created function.
    */
   protected def syncFunction(newFunction: QFunction) = {
-    newFunction.isIntermediate = this.isIntermediate
     newFunction.analysisName = this.analysisName
     newFunction.qSettings = this.qSettings
     newFunction.jobTempDir = this.jobTempDir
@@ -249,6 +234,11 @@ trait ScatterGatherableFunction extends CommandLineFunction {
     }
   }
 
+  /**
+   * The scatter function.
+   */
+  private lazy val scatterFunction = newScatterFunction()
+
   /**
    * Returns a temporary directory under this scatter gather directory.
    * @param Sub directory under the scatter gather directory.
diff --git a/scala/src/org/broadinstitute/sting/queue/function/scattergather/SimpleTextGatherFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/scattergather/SimpleTextGatherFunction.scala
index 6e35221a5..cdd3c2ab2 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/scattergather/SimpleTextGatherFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/scattergather/SimpleTextGatherFunction.scala
@@ -1,23 +1,14 @@
 package org.broadinstitute.sting.queue.function.scattergather
 
-import org.broadinstitute.sting.commandline.Argument
 import org.broadinstitute.sting.queue.function.InProcessFunction
-import org.apache.commons.io.FileUtils
 import org.broadinstitute.sting.queue.QException
-import collection.JavaConversions._
 import java.io.PrintWriter
+import org.apache.commons.io.{LineIterator, IOUtils, FileUtils}
 
 /**
  * Merges a text file.
- * The script can be changed by setting rmdirScript.
- * By default uses mergeText.sh in Sting/shell.
- * The format of the call is <mergeTextScript> <file_output> <file_1> [.. <file_n>]
  */
 class SimpleTextGatherFunction extends GatherFunction with InProcessFunction {
-  @Argument(doc="merge text script")
-  var mergeTextScript = "mergeText.sh"
-
-
   def run() = {
     if (gatherParts.size < 1) {
       throw new QException("No files to gather to output: " + originalOutput)
@@ -25,38 +16,48 @@ class SimpleTextGatherFunction extends GatherFunction with InProcessFunction {
       FileUtils.copyFile(gatherParts(0), originalOutput)
     } else {
       val writer = new PrintWriter(originalOutput)
-      var startLine = 0
+      try {
+        var startLine = 0
 
-      val readerA = FileUtils.lineIterator(gatherParts(0))
-      val readerB = FileUtils.lineIterator(gatherParts(1))
-      var headersMatch = true
-      while (headersMatch) {
-        if (readerA.hasNext && readerB.hasNext) {
-          val headerA = readerA.nextLine
-          val headerB = readerB.nextLine
-          headersMatch = headerA == headerB
-          if (headersMatch) {
-            startLine += 1
-            writer.println(headerA)
+        val readerA = FileUtils.lineIterator(gatherParts(0))
+        val readerB = FileUtils.lineIterator(gatherParts(1))
+        try {
+          var headersMatch = true
+          while (headersMatch) {
+            if (readerA.hasNext && readerB.hasNext) {
+              val headerA = readerA.nextLine
+              val headerB = readerB.nextLine
+              headersMatch = headerA == headerB
+              if (headersMatch) {
+                startLine += 1
+                writer.println(headerA)
+              }
+            } else {
+              headersMatch = false
+            }
           }
-        } else {
-          headersMatch = false
+        } finally {
+          LineIterator.closeQuietly(readerA)
+          LineIterator.closeQuietly(readerB)
         }
-      }
-      readerA.close
-      readerB.close
 
-      for (file <- gatherParts) {
-        val reader = FileUtils.lineIterator(file)
-        var lineNum = 0
-        while (reader.hasNext && lineNum < startLine) {
-          reader.nextLine
-          lineNum += 1
+        for (file <- gatherParts) {
+          val reader = FileUtils.lineIterator(file)
+          try {
+            var lineNum = 0
+            while (reader.hasNext && lineNum < startLine) {
+              reader.nextLine
+              lineNum += 1
+            }
+            while (reader.hasNext)
+              writer.println(reader.nextLine)
+          } finally {
+            LineIterator.closeQuietly(reader)
+          }
         }
-        while (reader.hasNext)
-          writer.println(reader.nextLine)
+      } finally {
+        IOUtils.closeQuietly(writer)
       }
-      writer.close
     }
   }
 }
diff --git a/scala/src/org/broadinstitute/sting/queue/pipeline/BamProcessing.scala b/scala/src/org/broadinstitute/sting/queue/pipeline/BamProcessing.scala
index bbee47f44..41506b825 100755
--- a/scala/src/org/broadinstitute/sting/queue/pipeline/BamProcessing.scala
+++ b/scala/src/org/broadinstitute/sting/queue/pipeline/BamProcessing.scala
@@ -23,7 +23,7 @@ class BamProcessing(yaml: File, gatkJar: File, fixMatesJar: File) {
 
   trait StandardCommandLineGATK extends CommandLineGATK {
     this.reference_sequence = library.attributes.getProject.getReferenceFile
-    this.intervals = library.attributes.getProject.getIntervalList
+    this.intervals :+= library.attributes.getProject.getIntervalList
     this.DBSNP = library.attributes.getProject.getDbsnpFile
     this.memoryLimit = Some(2)
     this.jarFile = library.gatkJar
@@ -35,7 +35,7 @@ class BamProcessing(yaml: File, gatkJar: File, fixMatesJar: File) {
    */
   def StandardRealignerTargetCreator(bam: File, contigs: List[String], output: File) : RealignerTargetCreator = {
     var rtc = new RealignerTargetCreator with StandardCommandLineGATK
-    rtc.intervals = null
+    rtc.intervals = Nil
     rtc.intervalsString = contigs
     rtc.input_file :+= bam
     rtc.out = output
@@ -51,7 +51,7 @@ class BamProcessing(yaml: File, gatkJar: File, fixMatesJar: File) {
   def StandardIndelCleaner(bam: File, contigs: List[String], targets: File, outBam: File) : IndelRealigner = {
     var realigner = new IndelRealigner with StandardCommandLineGATK
     realigner.intervalsString = contigs
-    realigner.intervals = null
+    realigner.intervals = Nil
     realigner.input_file :+= bam
     realigner.out = outBam
     realigner.targetIntervals = targets
diff --git a/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala b/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala
index 81d1ee1ab..a0fd91351 100755
--- a/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala
+++ b/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala
@@ -23,7 +23,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
    */
   trait StandardCommandLineGATK extends CommandLineGATK {
     this.reference_sequence = vc.attributes.getProject.getReferenceFile
-    this.intervals = vc.attributes.getProject.getIntervalList
+    this.intervals :+= vc.attributes.getProject.getIntervalList
     this.DBSNP = vc.attributes.getProject.getDbsnpFile
     // set global memory limit on the low side. Additional input bams will affect it.
     this.memoryLimit = Some(2)
diff --git a/scala/src/org/broadinstitute/sting/queue/util/ReflectionUtils.scala b/scala/src/org/broadinstitute/sting/queue/util/ReflectionUtils.scala
index 6f6ffdcc7..f6a174dd6 100644
--- a/scala/src/org/broadinstitute/sting/queue/util/ReflectionUtils.scala
+++ b/scala/src/org/broadinstitute/sting/queue/util/ReflectionUtils.scala
@@ -19,6 +19,19 @@ object ReflectionUtils {
    */
   def hasAnnotation(field: Field, annotation: Class[_ <: Annotation]) = field.getAnnotation(annotation) != null
 
+  /**
+   * Returns true if clazz or one of its superclasses has the annotation.
+   * @param clazz Class to check.
+   * @param annotation Class of the annotation to look for.
+   * @return true if field has the annotation.
+   */
+  def hasAnnotation(clazz: Class[_], annotation: Class[_ <: Annotation]) = {
+    var foundAnnotation = false
+    while (!foundAnnotation && clazz != null)
+      foundAnnotation = (clazz.getAnnotation(annotation) != null)
+    foundAnnotation
+  }
+
   /**
    * Gets the annotation or throws an exception if the annotation is not found.
    * @param field Field to check.
@@ -26,9 +39,26 @@ object ReflectionUtils {
    * @return The annotation.
    */
   def getAnnotation[T <: Annotation](field: Field, annotation: Class[T]): T = {
-    if (!hasAnnotation(field, annotation))
-      throw new QException("Field %s is missing annotation %s".format(field, annotation))
-    field.getAnnotation(annotation).asInstanceOf[T]
+    field.getAnnotation(annotation) match {
+      case null =>
+        throw new QException("Field %s is missing annotation %s".format(field, annotation))
+      case fieldAnnotation => fieldAnnotation.asInstanceOf[T]
+    }
+  }
+
+  /**
+   * Gets the annotation or throws an exception if the annotation is not found.
+   * @param clazz Class to check.
+   * @param annotation Class of the annotation to look for.
+   * @return The annotation.
+   */
+  def getAnnotation[T <: Annotation](clazz: Class[_], annotation: Class[T]): T = {
+    var result: T = null.asInstanceOf[T]
+    while (result == null && clazz != null)
+      result = clazz.getAnnotation(annotation)
+    if (result == null)
+      throw new QException("Class %s is missing annotation %s".format(clazz, annotation))
+    result
   }
 
   /**
diff --git a/scala/test/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunctionUnitTest.scala b/scala/test/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunctionUnitTest.scala
new file mode 100644
index 000000000..d541f1aa0
--- /dev/null
+++ b/scala/test/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunctionUnitTest.scala
@@ -0,0 +1,234 @@
+package org.broadinstitute.sting.queue.extensions.gatk
+
+import collection.JavaConversions._
+import java.io.File
+import org.junit.{Before, Assert, Test}
+import org.broadinstitute.sting.BaseTest
+import org.broadinstitute.sting.utils.interval.IntervalUtils
+import org.broadinstitute.sting.utils.GenomeLocParser
+import org.broadinstitute.sting.queue.QException
+import net.sf.picard.reference.IndexedFastaSequenceFile
+
+class IntervalScatterFunctionUnitTest extends BaseTest {
+  private def reference = new File(BaseTest.b36KGReference)
+  private var header: IndexedFastaSequenceFile = _
+
+  @Before
+  def setup() {
+    header = new IndexedFastaSequenceFile(reference)
+    GenomeLocParser.setupRefContigOrdering(header.getSequenceDictionary())
+  }
+
+  @Test
+  def testBasicScatter = {
+    val chr1 = GenomeLocParser.parseGenomeInterval("1")
+    val chr2 = GenomeLocParser.parseGenomeInterval("2")
+    val chr3 = GenomeLocParser.parseGenomeInterval("3")
+
+    val files = (1 to 3).toList.map(index => new File(testDir + "basic." + index + ".intervals"))
+
+    IntervalScatterFunction.scatter(List("1", "2", "3"), files, reference, false)
+
+    val locs1 = IntervalUtils.parseIntervalArguments(List(files(0).toString), false)
+    val locs2 = IntervalUtils.parseIntervalArguments(List(files(1).toString), false)
+    val locs3 = IntervalUtils.parseIntervalArguments(List(files(2).toString), false)
+
+    Assert.assertEquals(1, locs1.size)
+    Assert.assertEquals(1, locs2.size)
+    Assert.assertEquals(1, locs3.size)
+
+    Assert.assertEquals(chr1, locs1.get(0))
+    Assert.assertEquals(chr2, locs2.get(0))
+    Assert.assertEquals(chr3, locs3.get(0))
+  }
+
+  @Test
+  def testScatterLessFiles = {
+    val chr1 = GenomeLocParser.parseGenomeInterval("1")
+    val chr2 = GenomeLocParser.parseGenomeInterval("2")
+    val chr3 = GenomeLocParser.parseGenomeInterval("3")
+    val chr4 = GenomeLocParser.parseGenomeInterval("4")
+
+    val files = (1 to 3).toList.map(index => new File(testDir + "less." + index + ".intervals"))
+
+    IntervalScatterFunction.scatter(List("1", "2", "3", "4"), files, reference, false)
+
+    val locs1 = IntervalUtils.parseIntervalArguments(List(files(0).toString), false)
+    val locs2 = IntervalUtils.parseIntervalArguments(List(files(1).toString), false)
+    val locs3 = IntervalUtils.parseIntervalArguments(List(files(2).toString), false)
+
+    Assert.assertEquals(2, locs1.size)
+    Assert.assertEquals(1, locs2.size)
+    Assert.assertEquals(1, locs3.size)
+
+    Assert.assertEquals(chr1, locs1.get(0))
+    Assert.assertEquals(chr2, locs1.get(1))
+    Assert.assertEquals(chr3, locs2.get(0))
+    Assert.assertEquals(chr4, locs3.get(0))
+  }
+
+  @Test(expected=classOf[QException])
+  def testScatterMoreFiles = {
+    val files = (1 to 3).toList.map(index => new File(testDir + "more." + index + ".intervals"))
+    IntervalScatterFunction.scatter(List("1", "2"), files, reference, false)
+  }
+
+  @Test
+  def testScatterIntervals = {
+    val intervals = List("1:1-2", "1:4-5", "2:1-1", "3:2-2")
+    val chr1a = GenomeLocParser.parseGenomeInterval("1:1-2")
+    val chr1b = GenomeLocParser.parseGenomeInterval("1:4-5")
+    val chr2 = GenomeLocParser.parseGenomeInterval("2:1-1")
+    val chr3 = GenomeLocParser.parseGenomeInterval("3:2-2")
+
+    val files = (1 to 3).toList.map(index => new File(testDir + "split." + index + ".intervals"))
+
+    IntervalScatterFunction.scatter(intervals, files, reference, true)
+
+    val locs1 = IntervalUtils.parseIntervalArguments(List(files(0).toString), false)
+    val locs2 = IntervalUtils.parseIntervalArguments(List(files(1).toString), false)
+    val locs3 = IntervalUtils.parseIntervalArguments(List(files(2).toString), false)
+
+    Assert.assertEquals(2, locs1.size)
+    Assert.assertEquals(1, locs2.size)
+    Assert.assertEquals(1, locs3.size)
+
+    Assert.assertEquals(chr1a, locs1.get(0))
+    Assert.assertEquals(chr1b, locs1.get(1))
+    Assert.assertEquals(chr2, locs2.get(0))
+    Assert.assertEquals(chr3, locs3.get(0))
+  }
+
+
+  @Test
+  def testBasicScatterByContig = {
+    val chr1 = GenomeLocParser.parseGenomeInterval("1")
+    val chr2 = GenomeLocParser.parseGenomeInterval("2")
+    val chr3 = GenomeLocParser.parseGenomeInterval("3")
+
+    val files = (1 to 3).toList.map(index => new File(testDir + "contig_basic." + index + ".intervals"))
+
+    IntervalScatterFunction.scatter(List("1", "2", "3"), files, reference, true)
+
+    val locs1 = IntervalUtils.parseIntervalArguments(List(files(0).toString), false)
+    val locs2 = IntervalUtils.parseIntervalArguments(List(files(1).toString), false)
+    val locs3 = IntervalUtils.parseIntervalArguments(List(files(2).toString), false)
+
+    Assert.assertEquals(1, locs1.size)
+    Assert.assertEquals(1, locs2.size)
+    Assert.assertEquals(1, locs3.size)
+
+    Assert.assertEquals(chr1, locs1.get(0))
+    Assert.assertEquals(chr2, locs2.get(0))
+    Assert.assertEquals(chr3, locs3.get(0))
+  }
+
+  @Test
+  def testScatterByContigLessFiles = {
+    val chr1 = GenomeLocParser.parseGenomeInterval("1")
+    val chr2 = GenomeLocParser.parseGenomeInterval("2")
+    val chr3 = GenomeLocParser.parseGenomeInterval("3")
+    val chr4 = GenomeLocParser.parseGenomeInterval("4")
+
+    val files = (1 to 3).toList.map(index => new File(testDir + "contig_less." + index + ".intervals"))
+
+    IntervalScatterFunction.scatter(List("1", "2", "3", "4"), files, reference, true)
+
+    val locs1 = IntervalUtils.parseIntervalArguments(List(files(0).toString), false)
+    val locs2 = IntervalUtils.parseIntervalArguments(List(files(1).toString), false)
+    val locs3 = IntervalUtils.parseIntervalArguments(List(files(2).toString), false)
+
+    Assert.assertEquals(1, locs1.size)
+    Assert.assertEquals(1, locs2.size)
+    Assert.assertEquals(2, locs3.size)
+
+    Assert.assertEquals(chr1, locs1.get(0))
+    Assert.assertEquals(chr2, locs2.get(0))
+    Assert.assertEquals(chr3, locs3.get(0))
+    Assert.assertEquals(chr4, locs3.get(1))
+  }
+
+  @Test(expected=classOf[QException])
+  def testScatterByContigMoreFiles = {
+    val files = (1 to 3).toList.map(index => new File(testDir + "contig_more." + index + ".intervals"))
+    IntervalScatterFunction.scatter(List("1", "2"), files, reference, true)
+  }
+
+  @Test
+  def testScatterByContigIntervalsStart = {
+    val intervals = List("1:1-2", "1:4-5", "2:1-1", "3:2-2")
+    val chr1a = GenomeLocParser.parseGenomeInterval("1:1-2")
+    val chr1b = GenomeLocParser.parseGenomeInterval("1:4-5")
+    val chr2 = GenomeLocParser.parseGenomeInterval("2:1-1")
+    val chr3 = GenomeLocParser.parseGenomeInterval("3:2-2")
+
+    val files = (1 to 3).toList.map(index => new File(testDir + "contig_split_start." + index + ".intervals"))
+
+    IntervalScatterFunction.scatter(intervals, files, reference, true)
+
+    val locs1 = IntervalUtils.parseIntervalArguments(List(files(0).toString), false)
+    val locs2 = IntervalUtils.parseIntervalArguments(List(files(1).toString), false)
+    val locs3 = IntervalUtils.parseIntervalArguments(List(files(2).toString), false)
+
+    Assert.assertEquals(2, locs1.size)
+    Assert.assertEquals(1, locs2.size)
+    Assert.assertEquals(1, locs3.size)
+
+    Assert.assertEquals(chr1a, locs1.get(0))
+    Assert.assertEquals(chr1b, locs1.get(1))
+    Assert.assertEquals(chr2, locs2.get(0))
+    Assert.assertEquals(chr3, locs3.get(0))
+  }
+
+  @Test
+  def testScatterByContigIntervalsMiddle = {
+    val intervals = List("1:1-1", "2:1-2", "2:4-5", "3:2-2")
+    val chr1 = GenomeLocParser.parseGenomeInterval("1:1-1")
+    val chr2a = GenomeLocParser.parseGenomeInterval("2:1-2")
+    val chr2b = GenomeLocParser.parseGenomeInterval("2:4-5")
+    val chr3 = GenomeLocParser.parseGenomeInterval("3:2-2")
+
+    val files = (1 to 3).toList.map(index => new File(testDir + "contig_split_middle." + index + ".intervals"))
+
+    IntervalScatterFunction.scatter(intervals, files, reference, true)
+
+    val locs1 = IntervalUtils.parseIntervalArguments(List(files(0).toString), false)
+    val locs2 = IntervalUtils.parseIntervalArguments(List(files(1).toString), false)
+    val locs3 = IntervalUtils.parseIntervalArguments(List(files(2).toString), false)
+
+    Assert.assertEquals(1, locs1.size)
+    Assert.assertEquals(2, locs2.size)
+    Assert.assertEquals(1, locs3.size)
+
+    Assert.assertEquals(chr1, locs1.get(0))
+    Assert.assertEquals(chr2a, locs2.get(0))
+    Assert.assertEquals(chr2b, locs2.get(1))
+    Assert.assertEquals(chr3, locs3.get(0))
+  }
+
+  @Test
+  def testScatterByContigIntervalsEnd = {
+    val intervals = List("1:1-1", "2:2-2", "3:1-2", "3:4-5")
+    val chr1 = GenomeLocParser.parseGenomeInterval("1:1-1")
+    val chr2 = GenomeLocParser.parseGenomeInterval("2:2-2")
+    val chr3a = GenomeLocParser.parseGenomeInterval("3:1-2")
+    val chr3b = GenomeLocParser.parseGenomeInterval("3:4-5")
+
+    val files = (1 to 3).toList.map(index => new File(testDir + "contig_split_end." + index + ".intervals"))
+
+    IntervalScatterFunction.scatter(intervals, files, reference, true)
+
+    val locs1 = IntervalUtils.parseIntervalArguments(List(files(0).toString), false)
+    val locs2 = IntervalUtils.parseIntervalArguments(List(files(1).toString), false)
+    val locs3 = IntervalUtils.parseIntervalArguments(List(files(2).toString), false)
+
+    Assert.assertEquals(1, locs1.size)
+    Assert.assertEquals(1, locs2.size)
+    Assert.assertEquals(2, locs3.size)
+
+    Assert.assertEquals(chr1, locs1.get(0))
+    Assert.assertEquals(chr2, locs2.get(0))
+    Assert.assertEquals(chr3a, locs3.get(0))
+    Assert.assertEquals(chr3b, locs3.get(1))
+  }
+}