diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
index 13d90358b..19b4826bf 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
@@ -719,6 +719,7 @@ public class SlidingWindow {
         }
 
         for (GATKSAMRecord read : toRemove) {
+            removeFromHeader(windowHeader, read);
             readsInWindow.remove(read);
         }
         return hetReads;