diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
index 0512d487a..0d64c9e18 100644
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
@@ -251,6 +251,10 @@ public class GenomeAnalysisTK extends CommandLineProgram {
         try {
             LocusWalker<?, ?> walker = (LocusWalker<?, ?>) my_walker;
 
+            if ( REF_FILE_ARG == null )
+                Utils.scareUser(String.format("Locus-based traversals require a reference file but none was given"));
+
+
             if ( INPUT_FILE == null ) {
                 if ( walker.requiresReads() )
                     Utils.scareUser(String.format("Analysis %s requires reads, but none were given", Analysis_Name));
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
index 6bef0796e..0a3474a57 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
@@ -275,6 +275,7 @@ public abstract class TraversalEngine {
                     TraversalStatistics.nReads,
                     (TraversalStatistics.nSkippedReads * 100.0) / TraversalStatistics.nReads));
         logger.info(String.format("  -> %d unmapped reads", TraversalStatistics.nUnmappedReads));
+        logger.info(String.format("  -> %d duplicate reads", TraversalStatistics.nDuplicates));
         logger.info(String.format("  -> %d non-primary reads", TraversalStatistics.nNotPrimary));
         logger.info(String.format("  -> %d reads with bad alignments", TraversalStatistics.nBadAlignments));
         logger.info(String.format("  -> %d reads with indels", TraversalStatistics.nSkippedIndels));
@@ -490,6 +491,10 @@ public abstract class TraversalEngine {
                 TraversalStatistics.nBadAlignments++;
                 result = true;
                 why = "No alignment start";
+            } else if (rec.getDuplicateReadFlag()) {
+                TraversalStatistics.nDuplicates++;
+                result = true;
+                why = "Duplicate reads";
             }
             else {
                 result = false;
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalStatistics.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalStatistics.java
index 8c45ada90..2dfb9ad75 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalStatistics.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalStatistics.java
@@ -19,6 +19,7 @@ public class TraversalStatistics {
     public static int nNotPrimary;
     public static int nBadAlignments;
     public static int nSkippedIndels;
+    public static int nDuplicates;
 
     static {
         reset();
@@ -32,5 +33,6 @@ public class TraversalStatistics {
         nNotPrimary = 0;
         nBadAlignments = 0;
         nSkippedIndels = 0;
+        nDuplicates = 0;
     }
 }