diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
index c25517927..b9422b6e5 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
@@ -36,10 +36,7 @@ import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.*;
 
 import java.util.*;
 
@@ -273,15 +270,14 @@ public class ConsensusAlleleCounter {
             builder.alleles(Arrays.asList(refAllele, altAllele));
             builder.referenceBaseForIndel(ref.getBase());
             builder.noGenotypes();
-            if (doMultiAllelicCalls)
+            if (doMultiAllelicCalls) {
+                vcs.add(builder.make());
+                if (vcs.size() >= GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED)
+                    break;
+            } else if (curCnt > maxAlleleCnt) {
+                maxAlleleCnt = curCnt;
+                vcs.clear();
                 vcs.add(builder.make());
-            else {
-                if (curCnt > maxAlleleCnt) {
-                    maxAlleleCnt = curCnt;
-                    vcs.clear();
-                    vcs.add(builder.make());
-                }
-
             }
         }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 038414522..9036e3a62 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -217,8 +217,8 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
      **/
     public void initialize() {
         // check for a bad max alleles value
-        if ( UAC.MAX_ALTERNATE_ALLELES > GenotypeLikelihoods.MAX_ALLELES_THAT_CAN_BE_GENOTYPED )
-            throw new UserException.BadArgumentValue("max_alternate_alleles", "the maximum possible value is " + GenotypeLikelihoods.MAX_ALLELES_THAT_CAN_BE_GENOTYPED);
+        if ( UAC.MAX_ALTERNATE_ALLELES > GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED)
+            throw new UserException.BadArgumentValue("max_alternate_alleles", "the maximum possible value is " + GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED);
 
         // warn the user for misusing EMIT_ALL_SITES
         if ( UAC.OutputMode == UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES &&
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
index 63241f621..d950a4541 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
@@ -223,12 +223,12 @@ public class GenotypeLikelihoods {
     /**
      * The maximum number of alleles that we can represent as genotype likelihoods
      */
-    public final static int MAX_ALLELES_THAT_CAN_BE_GENOTYPED = 50;
+    public final static int MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED = 50;
 
     /*
      * a cache of the PL index to the 2 alleles it represents over all possible numbers of alternate alleles
      */
-    private final static GenotypeLikelihoodsAllelePair[] PLIndexToAlleleIndex = calculatePLcache(MAX_ALLELES_THAT_CAN_BE_GENOTYPED);
+    private final static GenotypeLikelihoodsAllelePair[] PLIndexToAlleleIndex = calculatePLcache(MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED);
 
     private static GenotypeLikelihoodsAllelePair[] calculatePLcache(final int altAlleles) {
         final int numLikelihoods = calculateNumLikelihoods(1+altAlleles, 2);
@@ -311,7 +311,7 @@ public class GenotypeLikelihoods {
     public static GenotypeLikelihoodsAllelePair getAllelePair(final int PLindex) {
         // make sure that we've cached enough data
         if ( PLindex >= PLIndexToAlleleIndex.length )
-            throw new ReviewedStingException("GATK limitation: cannot genotype more than " + MAX_ALLELES_THAT_CAN_BE_GENOTYPED + " alleles");
+            throw new ReviewedStingException("GATK limitation: cannot genotype more than " + MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED + " alleles");
 
         return PLIndexToAlleleIndex[PLindex];
     }