diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index ec31e1f2f..5c6e9dc01 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -374,7 +374,7 @@ public class UnifiedGenotyperEngine {
                                                  final VariantContext vc,
                                                  final GenotypeLikelihoodsCalculationModel.Model model,
                                                  final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
-        return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, false,perReadAlleleLikelihoodMap);
+        return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, false, perReadAlleleLikelihoodMap);
     }
 
     /**
diff --git a/protected/java/src/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java b/protected/java/src/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java
index 8ee3c166c..98aedf786 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java
@@ -46,6 +46,9 @@
 
 package org.broadinstitute.sting.utils.gvcf;
 
+import org.broadinstitute.sting.gatk.walkers.haplotypecaller.ReferenceConfidenceModel;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 import org.broadinstitute.variant.variantcontext.Genotype;
 import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
 import org.broadinstitute.variant.variantcontext.VariantContext;
@@ -284,7 +287,7 @@ public class GVCFWriter implements VariantContextWriter {
             }
 
             final Genotype g = vc.getGenotype(0);
-            if ( g.isHomRef() ) {
+            if ( g.isHomRef() && vc.hasAlternateAllele(GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE) ) {
                 // create bands
                 final VariantContext maybeCompletedBand = addHomRefSite(vc, g);
                 if ( maybeCompletedBand != null ) underlyingWriter.add(maybeCompletedBand);
diff --git a/protected/java/test/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java
index e353739e5..5c14c490e 100644
--- a/protected/java/test/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java
@@ -129,6 +129,16 @@ public class GVCFWriterUnitTest extends BaseTest {
         return vcb.genotypes(gb.make()).make();
     }
 
+    private VariantContext makeHomRefAlt(final String contig, final int start, final int GQ) {
+        final VariantContextBuilder vcb = new VariantContextBuilder("test", contig, start, start, Arrays.asList(REF, ALT));
+        final GenotypeBuilder gb = new GenotypeBuilder(SAMPLE_NAME, Arrays.asList(REF, REF));
+        gb.GQ(GQ);
+        gb.DP(10);
+        gb.AD(new int[]{1, 2});
+        gb.PL(new int[]{0, 10, 100});
+        return vcb.genotypes(gb.make()).make();
+    }
+
     private VariantContext makeNonRef(final String contig, final int start, final int GQ) {
         final VariantContextBuilder vcb = new VariantContextBuilder("test", contig, start, start, Arrays.asList(REF, ALT));
         final GenotypeBuilder gb = new GenotypeBuilder(SAMPLE_NAME, Arrays.asList(REF, ALT));
@@ -305,6 +315,25 @@ public class GVCFWriterUnitTest extends BaseTest {
         assertGoodVC(mockWriter.emitted.get(2), "20", 6, 7, false);
     }
 
+    @Test
+    public void testHomRefAlt() {
+        final GVCFWriter writer = new GVCFWriter(mockWriter, standardPartition);
+
+        writer.add(makeHomRef("20", 1, 0));
+        writer.add(makeHomRef("20", 2, 0));
+        writer.add(makeHomRefAlt("20", 3, 0));
+        writer.add(makeHomRef("20", 4, 0));
+        writer.add(makeHomRef("20", 5, 0));
+        writer.add(makeHomRef("20", 6, 0));
+        writer.add(makeHomRef("20", 7, 0));
+        writer.close();
+        Assert.assertEquals(mockWriter.emitted.size(), 3);
+        assertGoodVC(mockWriter.emitted.get(0), "20", 1, 2, false);
+        Assert.assertFalse(mockWriter.emitted.get(1).hasAttribute("END"));
+        Assert.assertFalse(mockWriter.emitted.get(1).hasAttribute("BLOCK_SIZE"));
+        assertGoodVC(mockWriter.emitted.get(2), "20", 4, 7, false);
+    }
+
     @DataProvider(name = "BandPartitionData")
     public Object[][] makeBandPartitionData() {
         List<Object[]> tests = new ArrayList<>();