diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java
index acbb2b10f..4b3c5f3de 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java
@@ -68,8 +68,6 @@ public class AnalyzeAnnotationsWalker extends RodWalker<Integer, Integer> {
     @Argument(fullName = "indicate_mean_num_vars", shortName = "meanNumVars", doc = "If supplied, plots will indicate the distribution of number of variants instead of distribution of value of annotation", required = false)
     private boolean INDICATE_MEAN_NUM_VARS = false;
         
-
-
     /////////////////////////////
     // Private Member Variables
     /////////////////////////////
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
index 80064ff67..d8c18db32 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
@@ -141,8 +141,11 @@ public class AnnotationDataManager {
 
             // Close the PrintStream
             output.close();
-            
-            String annotationName = nameMap.get(annotationKey);
+
+            String annotationName = null;
+            if( nameMap != null ) {
+                annotationName = nameMap.get(annotationKey);
+            }
             if( annotationName == null ) { // This annotation is not in the name map so use the key instead
                 annotationName = annotationKey;
             }