diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java
index 0f7b19743..84eb3e954 100755
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java
@@ -181,7 +181,7 @@ public class SAMDataSource implements SimpleDataSource {
      */
     private SamFileHeaderMerger createHeaderMerger() {
         List<SAMFileReader> lst = GetReaderList();
-        return new SamFileHeaderMerger(lst, SORT_ORDER);
+        return new SamFileHeaderMerger(lst, SORT_ORDER, true);
     }