diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java
index f78693c27..cc0a371ea 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java
@@ -73,8 +73,15 @@ public class IntervalSharder implements Iterator<FilePointer> {
      */
     public FilePointer next() {
         FilePointer current = wrappedIterator.next();
-        while(wrappedIterator.hasNext() && current.isRegionUnmapped == wrappedIterator.peek().isRegionUnmapped && current.minus(wrappedIterator.peek()) == 0)
+
+        while ( wrappedIterator.hasNext() &&
+                current.isRegionUnmapped == wrappedIterator.peek().isRegionUnmapped &&
+                (current.getContigIndex() == wrappedIterator.peek().getContigIndex() || current.isRegionUnmapped) &&
+                current.minus(wrappedIterator.peek()) == 0 ) {
+
             current = current.combine(parser,wrappedIterator.next());
+        }
+
         return current;
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardBalancer.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardBalancer.java
index 585b63457..e1bf2d98e 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardBalancer.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardBalancer.java
@@ -42,8 +42,10 @@ public class LocusShardBalancer extends ShardBalancer {
 
             public Shard next() {
                 FilePointer current = filePointers.next();
-                while(filePointers.hasNext() && current.minus(filePointers.peek()) == 0)
-                    current = current.combine(parser,filePointers.next());
+
+                // FilePointers have already been combined as necessary at the IntervalSharder level. No
+                // need to do so again here.
+
                 return new LocusShard(parser,readsDataSource,current.getLocations(),current.fileSpans);
             }