diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
index 6ea735ec0..9df92ba7a 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
@@ -334,10 +334,10 @@ public class GenotypingEngine {
                     boolean isBiallelic = true;
                     VariantContext thisVC = null;
                     VariantContext nextVC = null;
-                    int x11 = 0;
-                    int x12 = 0;
-                    int x21 = 0;
-                    int x22 = 0;
+                    double x11 = Double.NEGATIVE_INFINITY;
+                    double x12 = Double.NEGATIVE_INFINITY;
+                    double x21 = Double.NEGATIVE_INFINITY;
+                    double x22 = Double.NEGATIVE_INFINITY;
 
                     for( final Haplotype h : haplotypes ) {
                         // only make complex substitutions out of consecutive biallelic sites
@@ -360,13 +360,17 @@ public class GenotypingEngine {
                             }
                         }
                         // count up the co-occurrences of the events for the R^2 calculation
-                        // BUGBUG: use haplotype likelihoods per-sample to make this more accurate
-                        if( thisHapVC == null ) {
-                            if( nextHapVC == null ) { x11++; }
-                            else { x12++; }
-                        } else {
-                            if( nextHapVC == null ) { x21++; }
-                            else { x22++; }
+                        final ArrayList<Haplotype> haplotypeList = new ArrayList<Haplotype>();
+                        haplotypeList.add(h);
+                        for( final String sample : haplotypes.get(0).getSampleKeySet() ) {
+                            final double haplotypeLikelihood = LikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods( haplotypeList, sample )[0][0];
+                            if( thisHapVC == null ) {
+                                if( nextHapVC == null ) { x11 = MathUtils.approximateLog10SumLog10(x11, haplotypeLikelihood); }
+                                else { x12 = MathUtils.approximateLog10SumLog10(x12, haplotypeLikelihood); }
+                            } else {
+                                if( nextHapVC == null ) { x21 = MathUtils.approximateLog10SumLog10(x21, haplotypeLikelihood); }
+                                else { x22 = MathUtils.approximateLog10SumLog10(x22, haplotypeLikelihood); }
+                            }
                         }
                     }
                     if( thisVC == null || nextVC == null ) {
@@ -374,7 +378,7 @@ public class GenotypingEngine {
                         //throw new ReviewedStingException("StartPos TreeSet has an entry for an event that is found on no haplotype. start pos = " + thisStart + ", next pos = " + nextStart);
                     }
                     if( isBiallelic ) {
-                        final double R2 = calculateR2LD( x11, x12, x21, x22 );
+                        final double R2 = calculateR2LD( Math.pow(10.0, x11), Math.pow(10.0, x12), Math.pow(10.0, x21), Math.pow(10.0, x22) );
                         if( DEBUG ) {
                             System.out.println("Found consecutive biallelic events with R^2 = " + String.format("%.4f", R2));
                             System.out.println("-- " + thisVC);
@@ -445,12 +449,11 @@ public class GenotypingEngine {
         return new VariantContextBuilder("merged", thisVC.getChr(), thisVC.getStart() + iii, nextVC.getEnd(), mergedAlleles).make();
     }
 
-    @Requires({"x11 >= 0", "x12 >= 0", "x21 >= 0", "x22 >= 0"})
-    protected static double calculateR2LD( final int x11, final int x12, final int x21, final int x22 ) {
-        final int total = x11 + x12 + x21 + x22;
-        final double pa1b1 = ((double) x11) / ((double) total);
-        final double pa1b2 = ((double) x12) / ((double) total);
-        final double pa2b1 = ((double) x21) / ((double) total);
+    protected static double calculateR2LD( final double x11, final double x12, final double x21, final double x22 ) {
+        final double total = x11 + x12 + x21 + x22;
+        final double pa1b1 = x11 / total;
+        final double pa1b2 = x12 / total;
+        final double pa2b1 = x21 / total;
         final double pa1 = pa1b1 + pa1b2;
         final double pb1 = pa1b1 + pa2b1;
         return ((pa1b1 - pa1*pb1) * (pa1b1 - pa1*pb1)) / ( pa1 * (1.0 - pa1) * pb1 * (1.0 - pb1) );
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 14ea17483..1130feaea 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
@@ -415,7 +415,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
         likelihoodCalculationEngine.computeReadLikelihoods( haplotypes, perSampleReadList );
 
         // 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 ) : haplotypes );
+        final ArrayList<Haplotype> bestHaplotypes = haplotypes;// ( UG_engine.getUAC().GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? likelihoodCalculationEngine.selectBestHaplotypes( haplotypes ) : haplotypes );
 
         for( final Pair<VariantContext, HashMap<Allele, ArrayList<Haplotype>>> callResult :
                 ( GENOTYPE_FULL_ACTIVE_REGION && UG_engine.getUAC().GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES
@@ -496,7 +496,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
     //---------------------------------------------------------------------------------------------------------------
 
     private void finalizeActiveRegion( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) {
-        if( DEBUG ) { System.out.println("\nAssembling " + activeRegion.getExtendedLoc() + " with " + activeRegion.size() + " reads:"); }
+        if( DEBUG ) { System.out.println("\nAssembling " + activeRegion.getLocation() + " with " + activeRegion.size() + " reads:    (with overlap region = " + activeRegion.getExtendedLoc() + ")"); }
         final ArrayList<GATKSAMRecord> finalizedReadList = new ArrayList<GATKSAMRecord>();
         final FragmentCollection<GATKSAMRecord> fragmentCollection = FragmentUtils.create( ReadUtils.sortReadsByCoordinate(activeRegion.getReads()) );
         activeRegion.clearReads();
@@ -525,7 +525,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
     private List<GATKSAMRecord> filterNonPassingReads( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) {
         final ArrayList<GATKSAMRecord> readsToRemove = new ArrayList<GATKSAMRecord>();
         for( final GATKSAMRecord rec : activeRegion.getReads() ) {
-            if( rec.getReadLength() < 24 || rec.getMappingQuality() <= 20 || BadMateFilter.hasBadMate(rec) || (keepRG != null && !rec.getReadGroup().getId().equals(keepRG)) ) {
+            if( rec.getReadLength() < 24 || rec.getMappingQuality() < 20 || BadMateFilter.hasBadMate(rec) || (keepRG != null && !rec.getReadGroup().getId().equals(keepRG)) ) {
                 readsToRemove.add(rec);
             }
         }