diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
index f9518a35c..d833e9f8e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
@@ -47,7 +47,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
                                         final double[][] log10AlleleFrequencyPriors,
                                         final AlleleFrequencyCalculationResult result) {
 
-        final GenotypesContext GLs = vc.getGenotypes();
+        GenotypesContext GLs = vc.getGenotypes();
         List<Allele> alleles = vc.getAlleles();
 
         // don't try to genotype too many alternate alleles
@@ -58,7 +58,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
             alleles.add(vc.getReference());
             for ( int i = 0; i < MAX_ALTERNATE_ALLELES_TO_GENOTYPE; i++ )
                 alleles.add(vc.getAlternateAllele(i));
-            UnifiedGenotyperEngine.subsetAlleles(vc, alleles, false);
+            GLs = UnifiedGenotyperEngine.subsetAlleles(vc, alleles, false);
         }
 
         //linearExact(GLs, log10AlleleFrequencyPriors[0], log10AlleleFrequencyLikelihoods, log10AlleleFrequencyPosteriors);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index aa5776007..c84c944b8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -795,6 +795,10 @@ public class UnifiedGenotyperEngine {
         // then we can keep the PLs as is; otherwise, we determine which ones to keep
         if ( numNewAltAlleles != numOriginalAltAlleles && numNewAltAlleles > 0 ) {
             likelihoodIndexesToUse = new ArrayList<Integer>(30);
+
+            // make sure that we've cached enough data
+            if ( numOriginalAltAlleles > PLIndexToAlleleIndex.length - 1 )
+                calculatePLcache(numOriginalAltAlleles);
             final int[][] PLcache = PLIndexToAlleleIndex[numOriginalAltAlleles];
 
             final boolean[] altAlleleIndexToUse = new boolean[numOriginalAltAlleles];
@@ -834,20 +838,29 @@ public class UnifiedGenotyperEngine {
                 newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true);
             }
 
-            // if there is no mass on the (new) likelihoods or we weren't asked to assign a genotype, then just no-call the sample
-            if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > SUM_GL_THRESH_NOCALL ) {
+            // if there is no mass on the (new) likelihoods, then just no-call the sample
+            if ( MathUtils.sum(newLikelihoods) > SUM_GL_THRESH_NOCALL ) {
                 newGTs.add(new Genotype(g.getSampleName(), NO_CALL_ALLELES, Genotype.NO_LOG10_PERROR, null, null, false));
-                continue;
             }
+            else {
+                Map<String, Object> attrs = new HashMap<String, Object>(g.getAttributes());
+                if ( numNewAltAlleles == 0 )
+                    attrs.remove(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY);
+                else
+                    attrs.put(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, GenotypeLikelihoods.fromLog10Likelihoods(newLikelihoods));
 
-            final Genotype newGT = assignGenotype(g, newLikelihoods, allelesToUse, numNewAltAlleles);
-            newGTs.add(newGT);
+                // if we weren't asked to assign a genotype, then just no-call the sample
+                if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > SUM_GL_THRESH_NOCALL )
+                    newGTs.add(new Genotype(g.getSampleName(), NO_CALL_ALLELES, Genotype.NO_LOG10_PERROR, null, attrs, false));
+                else
+                    newGTs.add(assignGenotype(g, newLikelihoods, allelesToUse, numNewAltAlleles, attrs));
+            }
         }
         
         return newGTs;
     }
      
-    protected static Genotype assignGenotype(Genotype originalGT, double[] newLikelihoods, List<Allele> allelesToUse, int numNewAltAlleles) {
+    protected static Genotype assignGenotype(Genotype originalGT, double[] newLikelihoods, List<Allele> allelesToUse, int numNewAltAlleles, Map<String, Object> attrs) {
         // find the genotype with maximum likelihoods
         int PLindex = numNewAltAlleles == 0 ? 0 : MathUtils.maxElementIndex(newLikelihoods);
         int[] alleles = PLIndexToAlleleIndex[numNewAltAlleles][PLindex];
@@ -857,11 +870,6 @@ public class UnifiedGenotyperEngine {
         myAlleles.add(allelesToUse.get(alleles[1]));
 
         final double qual = numNewAltAlleles == 0 ? Genotype.NO_LOG10_PERROR : GenotypeLikelihoods.getQualFromLikelihoods(PLindex, newLikelihoods);
-        Map<String, Object> attrs = new HashMap<String, Object>(originalGT.getAttributes());
-        if ( numNewAltAlleles == 0 )
-            attrs.remove(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY);
-        else
-            attrs.put(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, GenotypeLikelihoods.fromLog10Likelihoods(newLikelihoods));
         return new Genotype(originalGT.getSampleName(), myAlleles, qual, null, attrs, false);
     }
 }
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 fd6738123..125242a2f 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
@@ -300,7 +300,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2.20101123.indels.sites.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,080,000", 1,
-                Arrays.asList("d356cbaf240d7025d1aecdabaff3a3e0"));
+                Arrays.asList("e4d2904b406f37d99fbe8f52ae75254f"));
         executeTest("test MultiSample Pilot2 indels with complicated records", spec3);
     }
 
@@ -309,7 +309,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec4 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2_chr20_100_110K.20101123.indels.sites.vcf -I " + validationDataLocation +
                         "phase1_GBR_realigned.chr20.100K-110K.bam -o %s -L 20:100,000-110,000", 1,
-                Arrays.asList("1d1956fd7b0f0d30935674b2f5019860"));
+                Arrays.asList("21f7b6c8b7eaccad1754a832bac79a65"));
         executeTest("test MultiSample Phase1 indels with complicated records", spec4);
     }