diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
index 2c7902914..fdfca982c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
@@ -56,11 +56,6 @@ import java.util.Set;
  * A variant set to filter.
  * </p>
  *
- * <h2>Output</h2>
- * <p>
- * A filtered VCF.
- * </p>
- *
  * <h2>Examples</h2>
  * <pre>
  * java -Xmx2g -jar GenomeAnalysisTK.jar \
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index 699133e38..1c65102ae 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -1085,14 +1085,15 @@ public class VariantContext implements Feature { // to enable tribble intergrati
     }
 
     public void validateReferenceBases(Allele reference, Byte paddedRefBase) {
-        // don't validate if we're an insertion or complex event
-        if ( !reference.isNull() && getReference().length() == 1 && !reference.basesMatch(getReference()) ) {
-            throw new TribbleException.InternalCodecException(String.format("the REF allele is incorrect for the record at position %s:%d, %s vs. %s", getChr(), getStart(), reference.getBaseString(), getReference().getBaseString()));
+        // don't validate if we're a complex event
+        if ( !isComplexIndel() && !reference.isNull() && !reference.basesMatch(getReference()) ) {
+            throw new TribbleException.InternalCodecException(String.format("the REF allele is incorrect for the record at position %s:%d, fasta says %s vs. VCF says %s", getChr(), getStart(), reference.getBaseString(), getReference().getBaseString()));
         }
 
         // we also need to validate the padding base for simple indels
-        if ( hasReferenceBaseForIndel() && !getReferenceBaseForIndel().equals(paddedRefBase) )
-            throw new TribbleException.InternalCodecException(String.format("the padded REF base is incorrect for the record at position %s:%d, %s vs. %s", getChr(), getStart(), (char)getReferenceBaseForIndel().byteValue(), (char)paddedRefBase.byteValue()));
+        if ( hasReferenceBaseForIndel() && !getReferenceBaseForIndel().equals(paddedRefBase) ) {
+            throw new TribbleException.InternalCodecException(String.format("the padded REF base is incorrect for the record at position %s:%d, fasta says %s vs. VCF says %s", getChr(), getStart(), (char)paddedRefBase.byteValue(), (char)getReferenceBaseForIndel().byteValue()));
+        }
     }
 
     public void validateRSIDs(Set<String> rsIDs) {