diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModelUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModelUnitTest.java
index 306dddd65..0731d3fd8 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModelUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModelUnitTest.java
@@ -109,4 +109,19 @@ public class ExactAFCalculationModelUnitTest extends BaseTest {
         int calculatedAlleleCount = result.getAlleleCountsOfMAP()[0];
         Assert.assertEquals(calculatedAlleleCount, 6);
     }
+
+    @Test
+    public void testMismatchedGLs() {
+
+        final double[] AB = new double[]{-2000.0, 0.0, -2000.0, -2000.0, -2000.0, -2000.0};
+        final double[] AC = new double[]{-100.0, -100.0, -100.0, 0.0, -100.0, -100.0};
+        GetGLsTest cfg = new GetGLsTest("B1C1", 2, createGenotype("1", AC), createGenotype("2", AB));
+
+        final AlleleFrequencyCalculationResult result = new AlleleFrequencyCalculationResult(2);
+
+        ExactAFCalculationModel.linearExactMultiAllelic(cfg.GLs, cfg.numAltAlleles, priors, result);
+
+        Assert.assertEquals(result.getAlleleCountsOfMAP()[0], 1);
+        Assert.assertEquals(result.getAlleleCountsOfMAP()[1], 1);
+    }
 }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index 2f0bfb507..99b62fa8d 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -60,7 +60,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultipleSNPAlleles() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
-                Arrays.asList("8472b1ad2fe1060e732da9e29d10cf99"));
+                Arrays.asList("cceb34ffbd2dbc45b8821f86ea255284"));
         executeTest("test Multiple SNP alleles", spec);
     }
 
@@ -76,10 +76,18 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testReverseTrim() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
-                Arrays.asList("8a4ad38ec8015eea3461295148143428"));
+                Arrays.asList("00f54a0097e710c0f7b001444c237e32"));
         executeTest("test reverse trim", spec);
     }
 
+    @Test
+    public void testMismatchedPLs() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
+                Arrays.asList("b3fae6bf4c620458f4259dbc93125e37"));
+        executeTest("test mismatched PLs", spec);
+    }
+
     // --------------------------------------------------------------------------------------------------------------
     //
     // testing compressed output
@@ -335,7 +343,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSampleIndels1() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
-                Arrays.asList("c3f786a5228346b43a80aa80d22b1490"));
+                Arrays.asList("af04b81f0548ca22b8d1f6bf223b336e"));
         List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(