diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
index 13852751a..b7af1d418 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -91,9 +91,9 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
             samples.add(sampleName.toUpperCase());
         }
 
-        // if there are no valid samples, die
+        // if there are no valid samples, warn the user
         if ( samples.size() == 0 )
-            throw new StingException("There are no samples input at all; use the --sampleName argument to specify one");
+            logger.warn("There are no samples input at all; use the --sampleName argument to specify one if desired.");
 
         determineAllAnnotations();