diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 7659c8a9e..2710aad25 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -293,7 +293,13 @@ public class GenomeAnalysisEngine {
         return outputTracker;
     }
 
-
+    /**
+     * This function is deprecated in the new traversal engines, if you need to get the header
+     * please get the engine and then use the getHeader function
+     *
+     * @return
+     */
+    @Deprecated
     public SAMFileReader getSamReader() {
         return this.engine.getSamReader();
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
index 5d92c5c2d..85ca68f13 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
@@ -590,6 +590,6 @@ public abstract class TraversalEngine {
                 logger.warn(msg);
         }
     }
-
+    @Deprecated
     public SAMFileReader getSamReader() { return this.samReader; }
 }