diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java
index 9165ac8cd..bf6c3ce1f 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java
@@ -37,10 +37,12 @@ public class MismatchHistoWalker extends ReadWalker<Integer, Integer> {
 
             int start = read.getAlignmentStart()-1;
             int stop  = read.getAlignmentEnd();
+            // sometimes BWA outputs screwy reads
+            if ( stop >= context.getReferenceContig().getBases().length )
+                return 0;
 
             List<Byte> refSeq = Utils.subseq(context.getReferenceContig().getBases(), start, stop);
             List<Byte> readBases = Utils.subseq(read.getReadBases());
-
             assert(refSeq.size() == readBases.size());
 
             // it's actually faster to reallocate a resized array than to use ArrayLists...
diff --git a/java/src/org/broadinstitute/sting/utils/Utils.java b/java/src/org/broadinstitute/sting/utils/Utils.java
index 81c3d1726..64d2b6738 100755
--- a/java/src/org/broadinstitute/sting/utils/Utils.java
+++ b/java/src/org/broadinstitute/sting/utils/Utils.java
@@ -163,6 +163,7 @@ public class Utils {
     }
 
     public static ArrayList<Byte> subseq(byte[] fullArray, int start, int end) {
+        assert end < fullArray.length;
         ArrayList<Byte> dest = new ArrayList<Byte>(end - start + 1);
         for (int i = start; i < end; i++) {
             dest.add(fullArray[i]);