diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
index cde089b34..acc76815e 100755
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
@@ -136,6 +136,10 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
     @Argument(fullName="gcpHMM", shortName="gcpHMM", doc="Flat gap continuation penalty for use in the Pair HMM", required = false)
     protected int gcpHMM = 10;
 
+    @Advanced
+    @Argument(fullName="maxNumHaplotypesInPopulation", shortName="maxNumHaplotypesInPopulation", doc="Maximum number of haplotypes to consider for your population. This number will probably need to be increased when calling organisms with high heterozygosity.", required = false)
+    protected int maxNumHaplotypesInPopulation = 13;
+
     @Advanced
     @Argument(fullName="minKmer", shortName="minKmer", doc="Minimum kmer length to use in the assembly graph", required = false)
     protected int minKmer = 11;
@@ -414,7 +418,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
         final Map<String, ArrayList<GATKSAMRecord>> perSampleFilteredReadList = splitReadsBySample( filteredReads );
 
         // subset down to only the best haplotypes to be genotyped in all samples ( in GGA mode use all discovered haplotypes )
-        final ArrayList<Haplotype> bestHaplotypes = ( UG_engine.getUAC().GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? likelihoodCalculationEngine.selectBestHaplotypes( haplotypes, stratifiedReadMap ) : haplotypes );
+        final ArrayList<Haplotype> bestHaplotypes = ( UG_engine.getUAC().GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ?
+                                                      likelihoodCalculationEngine.selectBestHaplotypes( haplotypes, stratifiedReadMap, maxNumHaplotypesInPopulation ) : haplotypes );
 
         for( final VariantContext call : genotypingEngine.assignGenotypeLikelihoods( UG_engine,
                                                                                      bestHaplotypes,
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
index e416b489b..6ca1ec1e8 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
@@ -273,7 +273,7 @@ public class LikelihoodCalculationEngine {
 
     @Requires({"haplotypes.size() > 0"})
     @Ensures({"result.size() <= haplotypes.size()"})
-    public ArrayList<Haplotype> selectBestHaplotypes( final ArrayList<Haplotype> haplotypes, final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap ) {
+    public ArrayList<Haplotype> selectBestHaplotypes( final ArrayList<Haplotype> haplotypes, final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap, final int maxNumHaplotypesInPopulation ) {
 
         final int numHaplotypes = haplotypes.size();
         final Set<String> sampleKeySet = stratifiedReadMap.keySet();
@@ -287,7 +287,7 @@ public class LikelihoodCalculationEngine {
         int hap1 = 0;
         int hap2 = 0;
         //double bestElement = Double.NEGATIVE_INFINITY;
-        final int maxChosenHaplotypes = Math.min( 13, sampleKeySet.size() * 2 + 1 );
+        final int maxChosenHaplotypes = Math.min( maxNumHaplotypesInPopulation, sampleKeySet.size() * 2 + 1 );
         while( bestHaplotypesIndexList.size() < maxChosenHaplotypes ) {
             double maxElement = Double.NEGATIVE_INFINITY;
             for( int iii = 0; iii < numHaplotypes; iii++ ) {