diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
index 4a3f12b44..90fe73575 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
@@ -238,8 +238,6 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<AssemblyBa
                 if( mergedVC == null )
                     continue;
 
-
-
                 final GenotypeLikelihoodsCalculationModel.Model calculationModel = mergedVC.isSNP()
                         ? GenotypeLikelihoodsCalculationModel.Model.SNP : GenotypeLikelihoodsCalculationModel.Model.INDEL;
 
@@ -286,6 +284,11 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<AssemblyBa
                         calledHaplotypes.addAll(haplotypeList);
                     }
 
+                    if ( !emitReferenceConfidence ) {
+                        // set GTs to no-call when GQ is 0 in normal mode
+                        annotatedCall = clearUnconfidentGenotypeCalls(annotatedCall);
+                    }
+
                     returnCalls.add( annotatedCall );
                 }
             }
@@ -809,4 +812,26 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<AssemblyBa
     public GenotypingModel getGenotypingModel() {
         return genotypingModel;
     }
+
+    /**
+     * Cleans up genotype-level annotations that need to be updated
+     * (similar to {@link org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs#cleanupGenotypeAnnotations},
+     * but here we only check for unconfident calls (i.e., those with GQ = 0), which are set to no-call).
+     */
+    private VariantContext clearUnconfidentGenotypeCalls(final VariantContext VC) {
+        final GenotypesContext oldGTs = VC.getGenotypes();
+        final List<Genotype> clearedGTs = new ArrayList<>(oldGTs.size());
+        for ( final Genotype oldGT : oldGTs ) {
+            // set GT to no-call when GQ is 0
+            if (oldGT.hasGQ() && oldGT.getGQ() == 0) {
+                final int ploidy = oldGT.getPloidy();
+                final List<Allele> noCallAlleles = GATKVariantContextUtils.noCallAlleles(ploidy);
+                final Genotype noCallGT = new GenotypeBuilder().alleles(noCallAlleles).make();
+                clearedGTs.add(noCallGT);
+            } else {
+                clearedGTs.add(oldGT);
+            }
+        }
+        return new VariantContextBuilder(VC).genotypes(clearedGTs).make();
+    }
 }
\ No newline at end of file
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
index 0a62bcdcb..42649af05 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
@@ -72,7 +72,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
 
     @Test
     public void testHaplotypeCallerMultiSampleComplex1() {
-        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "32ce23b3830f5f2c693161b40de8b15e");
+        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "88255eda0e29e4a6e128ddb7177a03ab");
     }
 
     private void HCTestSymbolicVariants(String bam, String args, String md5) {
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
index 4ff188851..2105366c0 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
@@ -126,7 +126,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
 
         // this functionality can be adapted to provide input data for whatever you might want in your data
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "0c87e26fdd7ab5629eb33f36833e3607"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "8bf132d73cf6b0851ae73c6799f19ba9"});
         tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "90b25f3050435c9e67aa0ee325c24167"});
         tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "5f329540dc5c4556ab029d0e2cfcabcb"});
         tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "6ad7855dbf6dda2060aa93a3ee010b3e"});
@@ -144,10 +144,10 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
 
         // this functionality can be adapted to provide input data for whatever you might want in your data
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "0820ae1d19ba0a2da25737ded8e2c96f"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "6662cfc41393257dfd6c39f1af1e3843"});
         tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "70ee4e60d9f86b63aaab09075a71ddd3"});
         tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "700d79df3b0b481444e81471204e242e"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "09d1ae38586465b98dea0a0e432a7146"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "af0fe243e3b96e59097187cd16ba1597"});
         tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "228e1d2ec2e729a5f79c37f3f2557708"});
         tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "2fc7020457dde4439b4133c098d9ab9b"});
 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 19d4a675b..168dde631 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -490,5 +490,15 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void testHBaseCountsBySample() throws IOException{
         HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A BaseCountsBySample", "f5ad4e03c0faaa806ee6ae536af8a479");
     }
+
+    @Test
+    public void testSetZeroGQsToNoCall() throws IOException{
+        final File testBAM = new File(privateTestDir + "set.zero.GQs.no.call.bam");
+        final String md5 = "b90da12d97fce42f5127bcb6cad07b09";
+        final String base = String.format("-T HaplotypeCaller  -R %s -I %s -L 8:17312375-17312975 ", REF, testBAM) +
+                " --no_cmdline_in_header -o %s";
+        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList(md5));
+        executeTest("testSetZeroGQsToNoCall", spec);
+    }
 }