diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/CountVariants.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/CountVariants.java
index f707e8479..139c16441 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/CountVariants.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/CountVariants.java
@@ -9,8 +9,6 @@ import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.utils.StingException;
 
-import java.util.List;
-import java.util.Arrays;
 
 @Analysis(name = "Count Variants", description = "Counts different classes of variants in the sample")
 public class CountVariants extends VariantEvaluator {
@@ -91,7 +89,7 @@ public class CountVariants extends VariantEvaluator {
     }
 
     public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        nProcessedLoci += context.getSkippedBases() + 1;
+        nProcessedLoci += context.getSkippedBases() + (ref == null ? 0 : 1);
     }
 
     public String update1(VariantContext vc1, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java
index 483007253..02f7c4dd9 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java
@@ -405,9 +405,6 @@ public class VariantEval2Walker extends RodWalker<Integer, Integer> {
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         //System.out.printf("map at %s with %d skipped%n", context.getLocation(), context.getSkippedBases());
 
-        if ( ref == null )
-            return 0;
-
         Map<String, VariantContext> vcs = getVariantContexts(tracker, context);
         //Collection<VariantContext> comps = getCompVariantContexts(tracker, context);
 
@@ -425,6 +422,10 @@ public class VariantEval2Walker extends RodWalker<Integer, Integer> {
                     // we always call update0 in case the evaluation tracks things like number of bases covered
                     evaluation.update0(tracker, ref, context);
 
+                    // the other updateN methods don't see a null context
+                    if ( tracker == null )
+                        continue;
+
                     // now call the single or paired update function
                     switch ( evaluation.getComparisonOrder() ) {
                         case 1:
@@ -444,7 +445,7 @@ public class VariantEval2Walker extends RodWalker<Integer, Integer> {
                 }
             }
 
-            if ( group.enableInterestingSiteCaptures && captureInterestingSitesOfEvalSet(group) )
+            if ( tracker != null && group.enableInterestingSiteCaptures && captureInterestingSitesOfEvalSet(group) )
                 writeInterestingSite(interestingReasons, vc, ref.getBase());
         }
 
@@ -536,8 +537,10 @@ public class VariantEval2Walker extends RodWalker<Integer, Integer> {
         // todo -- we need to deal with dbSNP where there can be multiple records at the same start site.  A potential solution is to
         // todo -- allow the variant evaluation to specify the type of variants it wants to see and only take the first such record at a site
         Map<String, VariantContext> bindings = new HashMap<String, VariantContext>();
-        bindVariantContexts(bindings, evalNames, tracker, context, false);
-        bindVariantContexts(bindings, compNames, tracker, context, true);
+        if ( tracker != null ) {
+            bindVariantContexts(bindings, evalNames, tracker, context, false);
+            bindVariantContexts(bindings, compNames, tracker, context, true);
+        }
         return bindings;
     }