diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
index 63aee013c..3ac64aa6a 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
@@ -43,7 +43,9 @@ import java.util.Arrays;
 public class AlleleBalance implements InfoFieldAnnotation, StandardAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
-
+        if ( stratifiedContexts.size() == 0 )
+            return null;
+        
         if ( !vc.isBiallelic() )
             return null;
         final Map<String, Genotype> genotypes = vc.getGenotypes();
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
index a016e9116..ca2de7047 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
@@ -17,6 +17,9 @@ import java.util.Arrays;
 public class DepthOfCoverage implements InfoFieldAnnotation, StandardAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
+        if ( stratifiedContexts.size() == 0 )
+            return null;
+
         int depth = 0;
         for ( String sample : stratifiedContexts.keySet() )
             depth += stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).size();
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
index a13f08abf..c7cfc0955 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
@@ -18,6 +18,9 @@ import java.util.Arrays;
 public class LowMQ implements InfoFieldAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
+        if ( stratifiedContexts.size() == 0 )
+            return null;
+
         double mq0 = 0;
 		double mq10 = 0;
 		double total = 0;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
index d9f7e684c..66322d36c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
@@ -19,6 +19,9 @@ import java.util.Arrays;
 public class MappingQualityZero implements InfoFieldAnnotation, StandardAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
+        if ( stratifiedContexts.size() == 0 )
+            return null;
+
         int mq0 = 0;
         for ( String sample : stratifiedContexts.keySet() ) {
             ReadBackedPileup pileup = stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
index 7099a5529..e21306ec8 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
@@ -17,6 +17,9 @@ import java.util.Arrays;
 public class QualByDepth implements InfoFieldAnnotation, StandardAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
+        if ( stratifiedContexts.size() == 0 )
+            return null;
+
         final Map<String, Genotype> genotypes = vc.getGenotypes();
         if ( genotypes == null || genotypes.size() == 0 )
             return null;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
index ca744bbbb..bdad04063 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
@@ -18,6 +18,9 @@ import java.util.*;
 public class RMSMappingQuality implements InfoFieldAnnotation, StandardAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
+        if ( stratifiedContexts.size() == 0 )
+            return null;
+
         ArrayList<Integer> qualities = new ArrayList<Integer>();
         for ( String sample : stratifiedContexts.keySet() ) {
             ReadBackedPileup pileup = stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
index 3156e75e4..3f230e49e 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
@@ -19,7 +19,9 @@ public abstract class RankSumTest implements InfoFieldAnnotation, WorkInProgress
     private static final double minPValue = 1e-10;
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
-
+        if ( stratifiedContexts.size() == 0 )
+            return null;
+         
         if ( !vc.isBiallelic() || !vc.isSNP() )
             return null;
         
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java
index 21f5045d4..01cdd9de2 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java
@@ -53,6 +53,9 @@ public class SecondBaseSkew implements InfoFieldAnnotation, ExperimentalAnnotati
     public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(KEY_NAME, 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Chi-square Secondary Base Skew")); }
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
+        if ( stratifiedContexts.size() == 0 )
+            return null;
+
         String annotation = getAnnotation(ref, stratifiedContexts, vc);
         if ( annotation == null )
             return null;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
index 2ff018b8d..403b22663 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
@@ -18,6 +18,9 @@ import java.util.Arrays;
 public class SpanningDeletions implements InfoFieldAnnotation, StandardAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
+        if ( stratifiedContexts.size() == 0 )
+            return null;
+
         int deletions = 0;
         int depth = 0;
         for ( String sample : stratifiedContexts.keySet() ) {
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
index 1d59e67d9..3589865fc 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -110,4 +110,11 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
     }
 
+    @Test
+    public void testNoReads() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -L 1:10,000,000-10,050,000", 1,
+                Arrays.asList("07af9983127c62e96accc03db2fb523e"));
+        executeTest("test file doesn't have annotations, not passing it any reads", spec);
+    }
 }
\ No newline at end of file