diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SimpleVenn.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SimpleVenn.java
index b02602bbf..f454e1e52 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SimpleVenn.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SimpleVenn.java
@@ -55,7 +55,7 @@ public class SimpleVenn implements ConcordanceType {
             printVariant(set2_writer, call2);
 
         // intersection (concordant)
-        else if ( call1.getAltBasesFWD().equals(call2.getAltBasesFWD()) )
+        else if ( call1.getAltBasesFWD().equalsIgnoreCase(call2.getAltBasesFWD()) )
             printVariant(intersect_writer, call1);
 
         // intersection (discordant)
@@ -74,4 +74,4 @@ public class SimpleVenn implements ConcordanceType {
         set1_writer.close();
         set2_writer.close();
     }
-}
\ No newline at end of file
+}