diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
index 987579ab8..6a825cba7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
@@ -59,10 +59,10 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
 
         int[][] table;
 
-        if (vc.isBiallelic() && vc.isSNP())
-            table = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAlternateAllele(0));
-        else if (vc.isIndel() || vc.isMixed()) {
-            table = getIndelContingencyTable(stratifiedContexts, vc);
+        if ( vc.isSNP() )
+            table = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount());
+        else if ( vc.isIndel() || vc.isMixed() ) {
+            table = getIndelContingencyTable(stratifiedContexts);
             if (table == null)
                 return null;
         }
@@ -234,7 +234,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
      *   allele2   #       #
      * @return a 2x2 contingency table
      */
-    private static int[][] getIndelContingencyTable(Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    private static int[][] getIndelContingencyTable(Map<String, AlignmentContext> stratifiedContexts) {
         final double INDEL_LIKELIHOOD_THRESH = 0.3;
         final HashMap<PileupElement,LinkedHashMap<Allele,Double>> indelLikelihoodMap = IndelGenotypeLikelihoodsCalculationModel.getIndelLikelihoodMap();
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index 27721be95..f5c57ca44 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -1229,12 +1229,15 @@ public class VariantContext implements Feature { // to enable tribble intergrati
     }
 
     public Allele getAltAlleleWithHighestAlleleCount() {
-        // first idea: get two alleles with highest AC
+        // optimization: for bi-allelic sites, just return the 1only alt allele
+        if ( isBiallelic() )
+            return getAlternateAllele(0);
+        
         Allele best = null;
         int maxAC1 = 0;
-        for (Allele a:this.getAlternateAlleles()) {
-            int ac = this.getCalledChrCount(a);
-            if (ac >=maxAC1) {
+        for ( Allele a : getAlternateAlleles() ) {
+            final int ac = getCalledChrCount(a);
+            if ( ac >= maxAC1 ) {
                 maxAC1 = ac;
                 best = a;
             }
@@ -1244,6 +1247,9 @@ public class VariantContext implements Feature { // to enable tribble intergrati
     }
 
     public int[] getGLIndecesOfAllele(Allele inputAllele) {
+
+        // TODO -- this information is cached statically by the UnifiedGenotyperEngine; pull it out into a common utils class for all to use
+
         int[] idxVector = new int[3];
         int numAlleles =  this.getAlleles().size();