diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
index 2deb6b8e5..667804194 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
@@ -215,7 +215,7 @@ public class VariantContextAdaptors {
         } else if ( !vcf.isIndel() ) {
             refAllele = Allele.create(ref.getBase(), true);
             if ( (char)ref.getBase() != vcf.getReference().charAt(0) )
-                System.err.println("\n*** WARN: The VCF reference base (" + vcf.getReference().charAt(0) + ") doesn't match the actual reference base (" + (char)ref.getBase() + "); there is a good chance this will generate an exception!");
+                throw new StingException("The VCF reference base (" + vcf.getReference().charAt(0) + ") doesn't match the actual reference base (" + (char)ref.getBase() + "); please check that you are using the appropriate reference file");
         } else if ( vcf.isDeletion() ) {
             int start = vcf.getPosition() - (int)ref.getWindow().getStart() + 1;
             int delLength = 0;