diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java
index f4c565318..59d496828 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java
@@ -100,7 +100,11 @@ public class GATKReport {
      * @param tableDescription  the description of the table
      */
     public void addTable(String tableName, String tableDescription) {
-        GATKReportTable table = new GATKReportTable(tableName, tableDescription);
+        addTable(tableName, tableDescription, true);
+    }
+
+    public void addTable(String tableName, String tableDescription, boolean sortByPrimaryKey) {
+        GATKReportTable table = new GATKReportTable(tableName, tableDescription, sortByPrimaryKey);
         tables.put(tableName, table);
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
index 0e503f92a..f7ea25696 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
@@ -3,9 +3,7 @@ package org.broadinstitute.sting.gatk.report;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.PrintStream;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.TreeSet;
+import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
@@ -96,8 +94,9 @@ public class GATKReportTable {
     private String tableDescription;
 
     private String primaryKeyName;
-    private TreeSet<Object> primaryKeyColumn;
+    private Collection<Object> primaryKeyColumn;
     private boolean primaryKeyDisplay;
+    boolean sortByPrimaryKey = true;
 
     private LinkedHashMap<String, GATKReportColumn> columns;
 
@@ -121,12 +120,17 @@ public class GATKReportTable {
      * @param tableDescription  the description of the table
      */
     public GATKReportTable(String tableName, String tableDescription) {
-        if (!isValidName(tableName)) {
+        this(tableName, tableDescription, true);
+    }
+
+    public GATKReportTable(String tableName, String tableDescription, boolean sortByPrimaryKey) {
+         if (!isValidName(tableName)) {
             throw new ReviewedStingException("Attempted to set a GATKReportTable name of '" + tableName + "'.  GATKReportTable names must be purely alphanumeric - no spaces or special characters are allowed.");
         }
 
         this.tableName = tableName;
         this.tableDescription = tableDescription;
+        this.sortByPrimaryKey = sortByPrimaryKey;
 
         columns = new LinkedHashMap<String, GATKReportColumn>();
     }
@@ -137,20 +141,14 @@ public class GATKReportTable {
      * @param primaryKeyName  the name of the primary key column
      */
     public void addPrimaryKey(String primaryKeyName) {
-        if (!isValidName(primaryKeyName)) {
-            throw new ReviewedStingException("Attempted to set a GATKReportTable primary key name of '" + primaryKeyName + "'.  GATKReportTable primary key names must be purely alphanumeric - no spaces or special characters are allowed.");
-        }
-
-        this.primaryKeyName = primaryKeyName;
-
-        primaryKeyColumn = new TreeSet<Object>();
-        primaryKeyDisplay = true;
+        addPrimaryKey(primaryKeyName, true);
     }
 
     /**
      * Add an optionally visible primary key column.  This becomes the unique identifier for every column in the table, and will always be printed as the first column.
      *
      * @param primaryKeyName  the name of the primary key column
+     * @param display should this primary key be displayed?
      */
     public void addPrimaryKey(String primaryKeyName, boolean display) {
         if (!isValidName(primaryKeyName)) {
@@ -159,7 +157,7 @@ public class GATKReportTable {
 
         this.primaryKeyName = primaryKeyName;
 
-        primaryKeyColumn = new TreeSet<Object>();
+        primaryKeyColumn = sortByPrimaryKey ? new TreeSet<Object>() : new LinkedList<Object>();
         primaryKeyDisplay = display;
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
index e3910ef11..89e20dad1 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
@@ -143,7 +143,7 @@ public class DiffEngine {
      * Not that only pairs of the same length are considered as potentially equivalent
      *
      * @param params determines how we display the items
-     * @param diffs
+     * @param diffs the list of differences to summarize
      */
     public void reportSummarizedDifferences(List<Difference> diffs, SummaryReportParams params ) {
         printSummaryReport(summarizeDifferences(diffs), params );
@@ -207,14 +207,7 @@ public class DiffEngine {
     }
 
     protected void printSummaryReport(List<Difference> sortedSummaries, SummaryReportParams params ) {
-        GATKReport report = new GATKReport();
-        final String tableName = "diffences";
-        report.addTable(tableName, "Summarized differences between the master and test files.\nSee http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine for more information");
-        GATKReportTable table = report.getTable(tableName);
-        table.addPrimaryKey("Difference", true);
-        table.addColumn("NumberOfOccurrences", 0);
-        table.addColumn("SpecificDifference", 0);
-
+        List<Difference> toShow = new ArrayList<Difference>();
         int count = 0, count1 = 0;
         for ( Difference diff : sortedSummaries ) {
             if ( diff.getCount() < params.minSumDiffToShow )
@@ -230,10 +223,26 @@ public class DiffEngine {
                     break;
             }
 
-            table.set(diff.getPath(), "NumberOfOccurrences", diff.getCount());
-            table.set(diff.getPath(), "SpecificDifference", diff.valueDiffString());
+            toShow.add(diff);
         }
 
+        // if we want it in descending order, reverse the list
+        if ( ! params.descending ) {
+            Collections.reverse(toShow);
+        }
+
+        // now that we have a specific list of values we want to show, display them
+        GATKReport report = new GATKReport();
+        final String tableName = "diffences";
+        report.addTable(tableName, "Summarized differences between the master and test files.\nSee http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine for more information", false);
+        GATKReportTable table = report.getTable(tableName);
+        table.addPrimaryKey("Difference", true);
+        table.addColumn("NumberOfOccurrences", 0);
+        table.addColumn("ExampleDifference", 0);
+        for ( Difference diff : toShow ) {
+            table.set(diff.getPath(), "NumberOfOccurrences", diff.getCount());
+            table.set(diff.getPath(), "ExampleDifference", diff.valueDiffString());
+        }
         table.write(params.out);
     }
 
@@ -252,7 +261,7 @@ public class DiffEngine {
      * commonPostfixLength: how many parts are shared at the end, suppose its 2
      * We want to create a string *.*.C.D
      *
-     * @param parts
+     * @param parts the separated path values [above without .]
      * @param commonPostfixLength
      * @return
      */
@@ -351,6 +360,7 @@ public class DiffEngine {
         int maxItemsToDisplay = 0;
         int maxCountOneItems = 0;
         int minSumDiffToShow = 0;
+        boolean descending = true;
 
         public SummaryReportParams(PrintStream out, int maxItemsToDisplay, int maxCountOneItems, int minSumDiffToShow) {
             this.out = out;
@@ -358,5 +368,9 @@ public class DiffEngine {
             this.maxCountOneItems = maxCountOneItems;
             this.minSumDiffToShow = minSumDiffToShow;
         }
+
+        public void setDescending(boolean descending) {
+            this.descending = descending;
+        }
     }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
index 8e362dcc4..fba6549fb 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
@@ -112,6 +112,7 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
         }
 
         DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(out, MAX_DIFFS, MAX_COUNT1_DIFFS, minCountForDiff);
+        params.setDescending(false);
         diffEngine.reportSummarizedDifferences(diffs, params);
     }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
index df2a5cda1..77a992ce0 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
@@ -72,13 +72,19 @@ public class VCFDiffableReader implements DiffableReader {
             }
 
             String line = lineReader.readLine();
-            int count = 0;
+            int count = 0, nRecordsAtPos = 1;
+            String prevName = "";
             while ( line != null ) {
                 if ( count++ > maxElementsToRead && maxElementsToRead != -1)
                     break;
 
                 VariantContext vc = (VariantContext)vcfCodec.decode(line);
                 String name = vc.getChr() + ":" + vc.getStart();
+                if ( name.equals(prevName) ) {
+                    name += "_" + ++nRecordsAtPos;
+                } else {
+                    prevName = name;
+                }
                 DiffNode vcRoot = DiffNode.empty(name, root);
 
                 // add fields
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java
index cca1eccb4..77159d9c2 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java
@@ -52,8 +52,8 @@ public class DiffObjectsIntegrationTest extends WalkerTest {
 
     @DataProvider(name = "data")
     public Object[][] createData() {
-        new TestParams(testDir + "diffTestMaster.vcf", testDir + "diffTestTest.vcf", "fb7f4e011487ca56bce865ae5468cdc5");
-        new TestParams(testDir + "exampleBAM.bam", testDir + "exampleBAM.simple.bam", "423cec3befbf0a72d8bc3757ee628fc4");
+        new TestParams(testDir + "diffTestMaster.vcf", testDir + "diffTestTest.vcf", "4d9f4636de05b93c354d05011264546e");
+        new TestParams(testDir + "exampleBAM.bam", testDir + "exampleBAM.simple.bam", "37e6efd833b5cd6d860a9df3df9713fc");
         return TestParams.getTests(TestParams.class);
     }