diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java
index 2780c3806..1bce6000c 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java
@@ -288,10 +288,15 @@ public class ReferenceConfidenceVariantContextMerger {
         for (final Allele a : vc.getAlternateAlleles()) {
             if (a.isSymbolic()) {
                 result.add(a);
-                // we always skip <NON_REF> when adding to finalAlleles; this is done outside if applies.
-                // we also skip <*DEL> if there isn't a real alternate allele.
+                // we always skip <NON_REF> when adding to finalAlleles; this is done outside if it applies.
+                // we also skip <*:DEL> if there isn't a real alternate allele.
                 if ( !a.equals(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE) && !vc.isSymbolic() )
                     finalAlleles.add(a);
+            } else if ( a == Allele.SPAN_DEL ) {
+                result.add(a);
+                // we skip * if there isn't a real alternate allele.
+                if ( !vc.isBiallelic() )
+                    finalAlleles.add(a);
             } else if (a.isCalled()) {
                 final Allele newAllele;
                 if (extraBaseCount > 0) {
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
index 601183705..73f410786 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
@@ -502,4 +502,16 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         spec.disableShadowBCF();
         executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec);
     }
+
+    @Test(enabled = true)
+    public void testGenotypingSpanningDeletionOverSpan() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
+                        " -V " + privateTestDir + "spanningDel.delOverSpan.1.g.vcf -V " +
+                        privateTestDir + "spanningDel.delOverSpan.2.g.vcf",
+                0,
+                Arrays.asList(""));     // we do not care about the md5; we just want to make sure it doesn't blow up with an error
+        spec.disableShadowBCF();
+        executeTest("testGenotypingSpanningDeletionOverSpan", spec);
+    }
 }
\ No newline at end of file