diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculator.java
index 1e720a6f5..68a88a717 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculator.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculator.java
@@ -194,7 +194,9 @@ import java.util.*;
                     }
                     gb.alleles(newAlleles);
                 }
-                if (combineAltAlleleLikelihoods(oldGenotype, genotypeCount, newLikelihoods, hetLikelihoods, homAltLikelihoods))
+                if (oldGenotype.isNonInformative())
+                    gb.PL(BIALLELIC_NON_INFORMATIVE_PLS);
+                else if (combineAltAlleleLikelihoods(oldGenotype, genotypeCount, newLikelihoods, hetLikelihoods, homAltLikelihoods))
                     gb.PL(newLikelihoods);
                 newGenotypes.add(gb.make());
             }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
index 9e524e347..791e4ac6d 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
@@ -140,7 +140,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
                         "low_coverage_CEU.chr1.10k-11k.bam -o %s -L " + result.get(0).getAbsolutePath(), 1,
-                Arrays.asList("f9d848fe5e6e6762e0dd5b5d925f74f4"));
+                Arrays.asList("08967b41ccc76b1f3c7093e51a90713a"));
         executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
     }
 
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 42649af05..383b85801 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", "", "88255eda0e29e4a6e128ddb7177a03ab");
+        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "113ae4c0244c50243313a7d6e77da26b");
     }
 
     private void HCTestSymbolicVariants(String bam, String args, String md5) {
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 04153ed2d..ef81bcf0a 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
@@ -157,7 +157,7 @@ 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,
-                Collections.singletonList("c2f30f25ba4a84e38c04aa49b95694e8"));
+                Collections.singletonList("af19ee0d7e739143be4e252c48701c45"));
         executeTest("combineSingleSamplePipelineGVCF_includeNonVariants", spec);
     }
 
@@ -579,7 +579,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                 baseTestString(" -V " + privateTestDir + "set.zero.RGQs.no.call.sample1.g.vcf" +
                         " -V " + privateTestDir + "set.zero.RGQs.no.call.sample2.g.vcf" +
                         " -L chr16:1279274-1279874 -allSites", hg19ReferenceWithChrPrefixInChromosomeNames),
-                Collections.singletonList("b7106be316e43ca04204b78038f65c9f"));
+                Collections.singletonList("92c097d8b6074d40f8d1385bc92a0a5d"));
         spec.disableShadowBCF();
         executeTest("testSetZeroRGQsToNoCall", spec);
     }