diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java
index 79e697227..ea7c4671c 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java
@@ -60,7 +60,6 @@ import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;
 import org.broadinstitute.gatk.engine.arguments.GenotypeCalculationArgumentCollection;
 import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
 import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
-import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.broadinstitute.gatk.utils.genotyper.IndexedSampleList;
 import org.broadinstitute.gatk.utils.genotyper.SampleList;
 import org.broadinstitute.gatk.utils.genotyper.SampleListUtils;
@@ -154,7 +153,7 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
      */
     @Advanced
     @Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to recompute.  The single value 'none' removes the default annotations", required=false)
-    protected List<String> annotationsToUse = new ArrayList<>(Arrays.asList(new String[]{"InbreedingCoeff", "FisherStrand", "QualByDepth", "ChromosomeCounts", "GenotypeSummaries", "StrandOddsRatio"}));
+    protected List<String> annotationsToUse = new ArrayList<>(Arrays.asList(new String[]{"InbreedingCoeff", "FisherStrand", "QualByDepth", "ChromosomeCounts", "StrandOddsRatio"}));
 
     /**
      * The rsIDs from this file are used to populate the ID column of the output.  Also, the DB INFO flag will be set when appropriate. Note that dbSNP is not used in any way for the calculations themselves.
@@ -215,6 +214,7 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
         // add the pool values for each genotype
         headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.MLE_ALLELE_COUNT_KEY));
         headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.MLE_ALLELE_FREQUENCY_KEY));
+        headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.REFERENCE_GENOTYPE_QUALITY));
         if ( dbsnp != null && dbsnp.dbsnp.isBound() )
             VCFStandardHeaderLines.addStandardInfoLines(headerLines, true, VCFConstants.DBSNP_KEY);
 
@@ -311,6 +311,7 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
      * 2. propagate DP to AD if not present
      * 3. remove SB if present
      * 4. change the PGT value from "0|1" to "1|1" for homozygous variant genotypes
+     * 5. move GQ to RGQ if the site is monomorphic
      *
      * @param VC            the VariantContext with the Genotypes to fix
      * @param createRefGTs  if true we will also create proper hom ref genotypes since we assume the site is monomorphic
@@ -332,6 +333,12 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
                 attrs.remove("MIN_DP");
             }
 
+            // move the GQ to RGQ
+            if ( createRefGTs && oldGT.hasGQ() ) {
+                builder.noGQ();
+                attrs.put(GATKVCFConstants.REFERENCE_GENOTYPE_QUALITY, oldGT.getGQ());
+            }
+
             // remove SB
             attrs.remove("SB");
 
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 33f163c5b..930932fd2 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
@@ -340,7 +340,7 @@ public class ReferenceConfidenceVariantContextMerger {
                             : genotypeIndexMapsByPloidy[ploidy];
                 final int[] PLs = generatePL(g, genotypeIndexMapByPloidy);
                 final int[] AD = g.hasAD() ? generateAD(g.getAD(), perSampleIndexesOfRelevantAlleles) : null;
-                genotypeBuilder.PL(PLs).AD(AD).noGQ();
+                genotypeBuilder.PL(PLs).AD(AD);
             }
             mergedGenotypes.add(genotypeBuilder.make());
         }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java
index 3f202dab4..51261fa69 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java
@@ -100,7 +100,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "tetraploid-gvcf-3.vcf" +
                         " -L " + privateTestDir + "tetraploid-gvcfs.intervals",
                 1,
-                Arrays.asList("20f55be01d01bed48bf66f354fa72e5b"));
+                Arrays.asList("7b3153135e4f8e1d137d3f4beb46f182"));
         executeTest("combineSingleSamplePipelineGVCF", spec);
     }
 
@@ -112,7 +112,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" +
                         " -L " + privateTestDir + "tetraploid-gvcfs.intervals",
                 1,
-                Arrays.asList("c8bf3da5eb641d0082bdd5f12ea58e1e"));
+                Arrays.asList("4f546634213ece6f08ec9258620b92bb"));
         executeTest("combineSingleSamplePipelineGVCF", spec);
     }
 
@@ -190,7 +190,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
     @Test
     public void testMD5s() throws Exception {
         final String cmd = baseTestString(" -L 1:69485-69791");
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("1df56fdfc71729cc82ba5dbfc75a72c4"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("b7c753452ab0c05f9cee538e420b87fa"));
         spec.disableShadowBCF();
         executeTest("testMD5s", spec);
     }
@@ -198,7 +198,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
     @Test
     public void testBasepairResolutionOutput() throws Exception {
         final String cmd = baseTestString(" -L 1:69485-69791 --convertToBasePairResolution");
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("9c8fc4d9e330fbe41a00b7f71a784f4e"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("bb6420ead95da4c72e76ca4bf5860ef0"));
         spec.disableShadowBCF();
         executeTest("testBasepairResolutionOutput", spec);
     }
@@ -206,7 +206,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
     @Test
     public void testBreakBlocks() throws Exception {
         final String cmd = baseTestString(" -L 1:69485-69791 --breakBandsAtMultiplesOf 5");
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("3a8e53b8b590eaa2675149ceccb80a7a"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("dd31182124c4b78a8a03edb1e0cf618b"));
         spec.disableShadowBCF();
         executeTest("testBreakBlocks", spec);
     }
@@ -215,7 +215,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
     public void testWrongReferenceBaseBugFix() throws Exception {
         final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -V " + (privateTestDir + "combine-gvcf-wrong-ref-input1.vcf"
                 + " -V " + (privateTestDir + "combine-gvcf-wrong-ref-input2.vcf") + " -o %s --no_cmdline_in_header");
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("04fa9d6084e4b3a7ea2ebe5675561e2f"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("75d81c247bef5e394b4a2d4126aee2b3"));
         spec.disableShadowBCF();
         executeTest("testWrongReferenceBaseBugFix",spec);
 
@@ -224,7 +224,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
     @Test
     public void testBasepairResolutionInput() throws Exception {
         final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -V " + privateTestDir + "gvcf.basepairResolution.vcf";
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("d3b3f0c8d8f8ef09475306a7814ddd38"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("994ff5c219c683635eadc1624cbbda74"));
         spec.disableShadowBCF();
         executeTest("testBasepairResolutionInput", spec);
     }
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 bdd7cdbf8..635b92a65 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
@@ -82,7 +82,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf", b37KGReference),
                 1,
-                Arrays.asList("6483df1dfa3a5290ba2dc10cc8e15370"));
+                Arrays.asList("91d0df8d9d57e573c32064b83510eb3e"));
         executeTest("testUpdatePGT", spec);
     }
 
@@ -91,7 +91,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf -A StrandAlleleCountsBySample", b37KGReference),
                 1,
-                Arrays.asList("4cbc86b7a44cf347eb543558de7b2ee6"));
+                Arrays.asList("88fa4a021e4aac9a0e48bd54b2949ece"));
         executeTest("testUpdatePGT, adding StrandAlleleCountsBySample annotation", spec);
     }
 
@@ -103,7 +103,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                         " -L 20:10,000,000-20,000,000", b37KGReference),
                 1,
-                Arrays.asList("d873327b474fa341cee7823a35efda89"));
+                Arrays.asList("56aef2d8c7e051cd8fa351474cd5ec10"));
         executeTest("combineSingleSamplePipelineGVCF", spec);
     }
 
@@ -115,7 +115,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "tetraploid-gvcf-3.vcf" +
                         " -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference),
                 1,
-                Arrays.asList("f5b3c4b4b45f7d3bc4a38ff5ac7076f0"));
+                Arrays.asList("599394c205c1d6641b9bebabbd29e13c"));
         executeTest("combineSingleSamplePipelineGVCF", spec);
     }
 
@@ -127,7 +127,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" +
                         " -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference),
                 1,
-                Arrays.asList("1f4632023ac646d7d04f65d797109f91"));
+                Arrays.asList("f7d5344a85e6d7fc2437d4253b424cb0"));
         executeTest("combineSingleSamplePipelineGVCF", spec);
     }
 
@@ -139,7 +139,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                         " --includeNonVariantSites -L 20:10,030,000-10,033,000 -L 20:10,386,000-10,386,500", b37KGReference),
                 1,
-                Arrays.asList("70376c02babc75c15a1e9a6be47e34fa"));
+                Arrays.asList("c9e4d1e52ee1f3a5233f1fb100f24d5e"));
         executeTest("combineSingleSamplePipelineGVCF_includeNonVariants", spec);
     }
 
@@ -152,7 +152,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                         " -L 20:10,000,000-20,000,000", b37KGReference),
                 1,
-                Arrays.asList("8c814998059fda80cf5a18242db13c19"));
+                Arrays.asList("0fc91d30c7de29c3507c8b9f9902c4f0"));
         executeTest("combineSingleSamplePipelineGVCFHierarchical", spec);
     }
 
@@ -164,7 +164,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                         " -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference),
                 1,
-                Arrays.asList("114a75003083cbe1a9966cc489d441af"));
+                Arrays.asList("f23c9d62542a69b5cbf0e9f89fdd235d"));
         executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec);
     }
 
@@ -174,7 +174,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                 "-T GenotypeGVCFs --no_cmdline_in_header -L 1:69485-69791 -o %s -R " + b37KGReference +
                 " -V " + privateTestDir + "gvcfExample1.vcf",
                 1,
-                Arrays.asList("364043ee77d4c6dfe1403a90b4938a65"));
+                Arrays.asList("97da49ef380f4b290095d6d2ac760393"));
         executeTest("testJustOneSample", spec);
     }
 
@@ -185,23 +185,24 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V " + privateTestDir + "gvcfExample1.vcf" +
                         " -V " + privateTestDir + "gvcfExample2.vcf",
                 1,
-                Arrays.asList("3fc58414196213bc3a85237b055b7883"));
+                Arrays.asList("654c4220c579e66e8b5e681267a3d795"));
         executeTest("testSamplesWithDifferentLs", spec);
     }
 
     @Test(enabled = true)
     public void testNoPLsException() {
         // Test with input files with (1) 0/0 and (2) ./.
+        final String md5 = "d04b32cf2fa97d303ff7fdc779a653d4";
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 "-T GenotypeGVCFs --no_cmdline_in_header -L 1:1115550-1115551 -o %s -R " + hg19Reference +
                         " --variant " + privateTestDir + "combined_genotype_gvcf_exception.vcf",
                 1,
-                Arrays.asList("08e4b839dede1b91ce6bd89c66ff063c"));
+                Arrays.asList(md5));
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 "-T GenotypeGVCFs --no_cmdline_in_header -L 1:1115550-1115551 -o %s -R " + hg19Reference +
                         " --variant " + privateTestDir + "combined_genotype_gvcf_exception.nocall.vcf",
                 1,
-                Arrays.asList("08e4b839dede1b91ce6bd89c66ff063c"));
+                Arrays.asList(md5));
         executeTest("testNoPLsException.1", spec1);
         executeTest("testNoPLsException.2", spec2);
     }
@@ -211,7 +212,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseBPResolutionString("-nda"),
                 1,
-                Arrays.asList("6bfc0d58eed9fc98642f36a09b1a235d"));
+                Arrays.asList("48636a1aa2cc38d5c22a28b68106433a"));
         executeTest("testNDA", spec);
     }
 
@@ -220,7 +221,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseBPResolutionString("-maxAltAlleles 1"),
                 1,
-                Arrays.asList("1e238c736e3f43e3693327a89455faaa"));
+                Arrays.asList("2bd7c520fb94f7f776973ad40b592a1a"));
         executeTest("testMaxAltAlleles", spec);
     }
 
@@ -229,7 +230,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseBPResolutionString("-stand_call_conf 300 -stand_emit_conf 100"),
                 1,
-                Arrays.asList("9c192402a005216649ff44a36cc7c45c"));
+                Arrays.asList("aa483875c5d36fd0115bb7e88f2ae5a7"));
         executeTest("testStandardConf", spec);
     }
 
@@ -273,7 +274,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:combined2 " + privateTestDir + "combine.single.sample.pipeline.combined.vcf" +
                         " --uniquifySamples", b37KGReference),
                 1,
-                Arrays.asList("ef6a96d57434bb63935fa7d9f012da9f"));
+                Arrays.asList("c285b05d52b2593ac22c2a123c7cc028"));
         executeTest("testUniquifiedSamples", spec);
 
     }
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java
index 1fe6aa208..6154b0bfb 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java
@@ -109,6 +109,7 @@ public final class GATKVCFConstants {
     public static final String HAPLOTYPE_CALLER_PHASING_GT_KEY =    "PGT";
     public static final String HAPLOTYPE_CALLER_PHASING_ID_KEY =    "PID";
     public static final String PHRED_SCALED_POSTERIORS_KEY =        "PP"; //FamilyLikelihoodsUtils / PosteriorLikelihoodsUtils
+    public static final String REFERENCE_GENOTYPE_QUALITY =         "RGQ";
     public static final String STRAND_COUNT_BY_SAMPLE_KEY =         "SAC";
     public static final String STRAND_BIAS_BY_SAMPLE_KEY =          "SB";
     public final static String TRANSMISSION_PROBABILITY_KEY =       "TP"; //PhaseByTransmission
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java
index fa8160e50..ccfd89b60 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java
@@ -78,6 +78,7 @@ public class GATKVCFHeaderLines {
         addFormatLine(new VCFFormatHeaderLine(HAPLOTYPE_CALLER_PHASING_ID_KEY, 1, VCFHeaderLineType.String, "Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"));
         addFormatLine(new VCFFormatHeaderLine(HAPLOTYPE_CALLER_PHASING_GT_KEY, 1, VCFHeaderLineType.String, "Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"));
         addFormatLine(new VCFFormatHeaderLine(MIN_DP_FORMAT_KEY, 1, VCFHeaderLineType.Integer, "Minimum DP observed within the GVCF block"));
+        addFormatLine(new VCFFormatHeaderLine(REFERENCE_GENOTYPE_QUALITY, 1, VCFHeaderLineType.Integer, "Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)"));
         addFormatLine(new VCFFormatHeaderLine(TRANSMISSION_PROBABILITY_KEY, 1, VCFHeaderLineType.Integer, "Phred score of the genotype combination and phase given that the genotypes are correct"));
         addFormatLine(new VCFFormatHeaderLine(RBP_HAPLOTYPE_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Read-backed phasing haplotype identifiers"));
         addFormatLine(new VCFFormatHeaderLine(AVG_INTERVAL_DP_BY_SAMPLE_KEY, 1, VCFHeaderLineType.Float, "Average sample depth across the interval. Sum of the sample specific depth in all loci divided by interval size."));