diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
index 219c36a05..989f06ec5 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
@@ -70,12 +70,12 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
-        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","7d6f319b9edcb1ff8c290fef150a2df8");
+        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","9acfe0019efdc91217ee070acb071228");
     }
 
     @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
-        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","dd02890123e07e7412a49475cb6280f1");
+        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","c1d4dd793f61710a1b1fc5d82803210f");
     }
 
     @Test(enabled = true)
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index be8fd2fb2..a8ea4b7da 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -21,7 +21,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerMultiSample() {
-        HCTest(CEUTRIO_BAM, "", "8c52c0955099cca3215a0d78fd455894");
+        HCTest(CEUTRIO_BAM, "", "75013fa6a884104f0b1797502b636698");
     }
 
     @Test
@@ -31,7 +31,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerMultiSampleGGA() {
-        HCTest(CEUTRIO_BAM, "--max_alternate_alleles_for_indels 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "61c1a0fb62d909229af6b5a91dad8b35");
+        HCTest(CEUTRIO_BAM, "--max_alternate_alleles_for_indels 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "3cd3363976b1937d801f9f82996f4abe");
     }
 
     private void HCTestComplexVariants(String bam, String args, String md5) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PerReadAlleleLikelihoodMap.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PerReadAlleleLikelihoodMap.java
index 9c0062876..a83adc275 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PerReadAlleleLikelihoodMap.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PerReadAlleleLikelihoodMap.java
@@ -113,23 +113,20 @@ public class PerReadAlleleLikelihoodMap {
         return likelihoodReadMap.get(p.getRead());
     }
 
-    public static Allele getMostLikelyAllele(Map<Allele,Double> alleleMap) {
-        double minLike = Double.POSITIVE_INFINITY, maxLike = Double.NEGATIVE_INFINITY;
+    public static Allele getMostLikelyAllele( final Map<Allele,Double> alleleMap ) {
+        double maxLike = Double.NEGATIVE_INFINITY;
+        double prevMaxLike = Double.NEGATIVE_INFINITY;
         Allele mostLikelyAllele = Allele.NO_CALL;
 
-        for (Map.Entry<Allele,Double> el : alleleMap.entrySet()) {
+        for (final Map.Entry<Allele,Double> el : alleleMap.entrySet()) {
             if (el.getValue() > maxLike) {
+                prevMaxLike = maxLike;
                 maxLike = el.getValue();
                 mostLikelyAllele = el.getKey();
+            } else if( el.getValue() > prevMaxLike ) {
+                prevMaxLike = el.getValue();
             }
-
-            if (el.getValue() < minLike)
-                minLike = el.getValue();
-
         }
-        if (maxLike-minLike > INDEL_LIKELIHOOD_THRESH)
-            return mostLikelyAllele;
-        else
-            return Allele.NO_CALL;
+        return (maxLike - prevMaxLike > INDEL_LIKELIHOOD_THRESH ? mostLikelyAllele : Allele.NO_CALL );
     }
  }
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 df088a4ad..72724e46a 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("26af30187316f742878c85f0ed091837"));
+                Arrays.asList("48b4f4b05461be276bffc91350f08cbc"));
         executeTest("test Multiple SNP alleles", spec);
     }
 
@@ -76,7 +76,7 @@ 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("aa9cf96ab8f5aa844387e3aef1f27249"));
+                Arrays.asList("04affcc9d720ee17bc221759707e0cd2"));
         executeTest("test reverse trim", spec);
     }
 
@@ -84,7 +84,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     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("d210ee1baa75dd4a0c63aef6b1fa7a8a"));
+                Arrays.asList("112e7bedfd284d4d9390aa006118c733"));
         executeTest("test mismatched PLs", spec);
     }
 
@@ -343,13 +343,13 @@ 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("7fc488fe16dea9f023bfcfdaa908a548"));
+                Arrays.asList("863ee56b3594f09795644127f2f9539f"));
         List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
 
         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 1:10450700-10551000", 1,
-                Arrays.asList("f3ff7fe0f15f31eadd726c711d6bf3de"));
+                Arrays.asList("503ca1b75cc7b2679eaa80f7b5e7ef1c"));
         executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
     }
 
@@ -452,5 +452,4 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                 Arrays.asList("bbf16e1873e525ee5975021cfb8988cf"));
         executeTest("test calling on a ReducedRead BAM", spec);
     }
-
 }