diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnEdge.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnEdge.java
index 39bb3617f..287acafb3 100755
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnEdge.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnEdge.java
@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
 
 import org.jgrapht.graph.DefaultDirectedGraph;
 
+import java.io.Serializable;
 import java.util.Comparator;
 
 /**
@@ -55,7 +56,7 @@ public class DeBruijnEdge {
         return (graph.getEdgeSource(this).equals(graph2.getEdgeSource(edge))) && (graph.getEdgeTarget(this).equals(graph2.getEdgeTarget(edge)));
     }
 
-    public static class EdgeWeightComparator implements Comparator<DeBruijnEdge> {
+    public static class EdgeWeightComparator implements Comparator<DeBruijnEdge>, Serializable {
         @Override
         public int compare(final DeBruijnEdge edge1, final DeBruijnEdge edge2) {
             return edge1.multiplicity - edge2.multiplicity;
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KBestPaths.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KBestPaths.java
index 4a5a906f2..f7575439b 100755
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KBestPaths.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KBestPaths.java
@@ -4,6 +4,7 @@ import org.apache.commons.lang.ArrayUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.jgrapht.graph.DefaultDirectedGraph;
 
+import java.io.Serializable;
 import java.util.*;
 
 /**
@@ -76,14 +77,14 @@ public class KBestPaths {
         }
     }
 
-    protected static class PathComparatorTotalScore implements Comparator<Path> {
+    protected static class PathComparatorTotalScore implements Comparator<Path>, Serializable {
         @Override
         public int compare(final Path path1, final Path path2) {
             return path1.totalScore - path2.totalScore;
         }
     }
 
-    //protected static class PathComparatorLowestEdge implements Comparator<Path> {
+    //protected static class PathComparatorLowestEdge implements Comparator<Path>, Serializable {
     //    @Override
     //    public int compare(final Path path1, final Path path2) {
     //        return path2.lowestEdge - path1.lowestEdge;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
index c6d8883c5..27a6c068f 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
@@ -47,6 +47,7 @@ import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
+import java.io.Serializable;
 import java.util.*;
 
 /**
@@ -103,7 +104,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
         return map;
     }
 
-    private static class HaplotypeComparator implements Comparator<Haplotype> {
+    private static class HaplotypeComparator implements Comparator<Haplotype>, Serializable {
 
         public int compare(Haplotype a, Haplotype b) {
             if (a.getQualitySum() < b.getQualitySum())
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
index 14ef63264..042d4741d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
@@ -29,10 +29,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
 
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.PrintStream;
+import java.io.*;
 import java.util.*;
 
 /**
@@ -83,7 +80,7 @@ public class Tranche {
         return accessibleTruthSites > 0 ? callsAtTruthSites / (1.0*accessibleTruthSites) : 0.0;
     }
 
-    public static class TrancheTruthSensitivityComparator implements Comparator<Tranche> {
+    public static class TrancheTruthSensitivityComparator implements Comparator<Tranche>, Serializable {
         @Override
         public int compare(final Tranche tranche1, final Tranche tranche2) {
             return Double.compare(tranche1.ts, tranche2.ts);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
index 55052f73b..7b3b0d17d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
 
+import java.io.Serializable;
 import java.util.Comparator;
 
 /**
@@ -54,7 +55,7 @@ public class VariantDatum {
     public int worstAnnotation;
     public MultivariateGaussian assignment; // used in K-means implementation 
 
-    public static class VariantDatumLODComparator implements Comparator<VariantDatum> {
+    public static class VariantDatumLODComparator implements Comparator<VariantDatum>, Serializable {
         @Override
         public int compare(final VariantDatum datum1, final VariantDatum datum2) {
             return Double.compare(datum1.lod, datum2.lod);
diff --git a/public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java b/public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java
index 99f43876c..8339e38c9 100755
--- a/public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java
+++ b/public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java
@@ -11,6 +11,7 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 
+import java.io.Serializable;
 import java.util.Comparator;
 import java.util.TreeSet;
 
@@ -434,12 +435,14 @@ public class MannWhitneyU {
      * A comparator class which uses dithering on tie-breaking to ensure that the internal treeset drops no values
      * and to ensure that rank ties are broken at random.
      */
-    private static class DitheringComparator implements Comparator<Pair<Number,USet>> {
+    private static class DitheringComparator implements Comparator<Pair<Number,USet>>, Serializable {
 
         public DitheringComparator() {}
 
+        @Override
         public boolean equals(Object other) { return false; }
 
+        @Override
         public int compare(Pair<Number,USet> left, Pair<Number,USet> right) {
             double comp = Double.compare(left.first.doubleValue(),right.first.doubleValue());
             if ( comp > 0 ) { return 1; }