diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java
index c6ee2e44e..14ad75aa3 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java
@@ -78,7 +78,7 @@ class TiTvRatioSample extends SampleDataPoint {
     }
 
     public void update2(VariantContext vc, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        if ( vc != null && vc.isSNP() ) {
+        if ( vc != null && vc.isSNP() && vc.isBiallelic() ) {
             if ( VariantContextUtils.isTransition(vc) ) {
                 nTi++;
             } else {
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java
index 8a7bfb18b..cd64beb37 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java
@@ -163,7 +163,7 @@ class EvalBySample implements TableType {
     }
 
     public void finalizeTable() {
-        finalizedResults = new Object[sampleAndEvalResults.size()][sampleAndEvalResults.size()];
+        finalizedResults = new Object[sampleAndEvalResults.size()][sampleAndEvalResults.firstEntry().getValue().size()];
         int i = 0;
         for ( Map.Entry<String,List<SampleDataPoint>> evalBySample : sampleAndEvalResults.entrySet() ) {
             int j = 0;