diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
index b3f3630bd..3c7c6f00c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
@@ -46,6 +46,7 @@ import java.util.*;
 public class VariantSummary extends VariantEvaluator implements StandardEval {
     final protected static Logger logger = Logger.getLogger(VariantSummary.class);
 
+    /** Indels with size greater than this value are tallied in the CNV column */
     private final static int MAX_INDEL_LENGTH = 50;
     private final static double MIN_CNV_OVERLAP = 0.5;
     private VariantEvalWalker walker;
@@ -196,14 +197,16 @@ public class VariantSummary extends VariantEvaluator implements StandardEval {
     }
 
     private final boolean overlapsKnownCNV(VariantContext cnv) {
-        final GenomeLoc loc = walker.getGenomeLocParser().createGenomeLoc(cnv, true);
-        IntervalTree<GenomeLoc> intervalTree = knownCNVs.get(loc.getContig());
+        if ( knownCNVs != null ) {
+            final GenomeLoc loc = walker.getGenomeLocParser().createGenomeLoc(cnv, true);
+            IntervalTree<GenomeLoc> intervalTree = knownCNVs.get(loc.getContig());
 
-        final Iterator<IntervalTree.Node<GenomeLoc>> nodeIt = intervalTree.overlappers(loc.getStart(), loc.getStop());
-        while ( nodeIt.hasNext() ) {
-            final double overlapP = loc.reciprocialOverlapFraction(nodeIt.next().getValue());
-            if ( overlapP > MIN_CNV_OVERLAP )
-                return true;
+            final Iterator<IntervalTree.Node<GenomeLoc>> nodeIt = intervalTree.overlappers(loc.getStart(), loc.getStop());
+            while ( nodeIt.hasNext() ) {
+                final double overlapP = loc.reciprocialOverlapFraction(nodeIt.next().getValue());
+                if ( overlapP > MIN_CNV_OVERLAP )
+                    return true;
+            }
         }
 
         return false;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
index b3555b145..5c3a43c96 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -450,4 +450,21 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                               );
         executeTest("testIntervalStrat", spec);
     }
+
+    @Test
+    public void testModernVCFWithLargeIndels() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                                buildCommandLine(
+                                        "-T VariantEval",
+                                        "-R " + b37KGReference,
+                                        "-eval " + validationDataLocation + "/NA12878.HiSeq.WGS.b37_decoy.indel.recalibrated.vcf",
+                                        "-L 20",
+                                        "-D " + b37dbSNP132,
+                                        "-o %s"
+                                ),
+                                1,
+                                Arrays.asList("a6f8b32fa732632da13dfe3ddcc73cef")
+                              );
+        executeTest("testModernVCFWithLargeIndels", spec);
+    }
 }