diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java
index 11a442b0b..b9fd32055 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java
@@ -61,6 +61,12 @@ public class MismatchIntervalWalker extends LocusWalker<Pair<GenomeLoc, Boolean>
     }
 
     public Pair<LinkedList<Boolean>, GenomeLoc> reduce(Pair<GenomeLoc, Boolean> value, Pair<LinkedList<Boolean>, GenomeLoc> sum) {
+        // if we hit a new contig, clear the list
+        if ( sum.second != null && sum.second.getContigIndex() != value.first.getContigIndex() ) {
+            sum.first.clear();
+            sum.second = null;
+        }
+        
         sum.first.addLast(value.second);
         if ( sum.first.size() <= windowSize )
             return sum;