diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
index e5f75f06d..3a21e97a4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
@@ -69,7 +69,7 @@ public class AlleleBalance extends InfoFieldAnnotation {
             if ( context == null )
                 continue;
 
-            if ( vc.isSNP() ) {
+            if ( vc.isSNP() && context.hasBasePileup() ) {
                 final String bases = new String(context.getBasePileup().getBases());
                 if ( bases.length() == 0 )
                     return null;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
index 820fd248a..06e91bf26 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
@@ -51,6 +51,9 @@ public class AlleleBalanceBySample extends GenotypeAnnotation implements Experim
         if ( altAlleles.size() == 0 )
             return null;
 
+        if ( !stratifiedContext.hasBasePileup() )
+            return null;
+
         final String bases = new String(stratifiedContext.getBasePileup().getBases());
         if ( bases.length() == 0 )
             return null;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
index fd55d78a0..e64d00bf5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
@@ -365,7 +365,7 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
             return counter;
 
         // Do not operate on variants that are not covered to the optional minimum depth
-        if (!context.hasReads() || (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) {
+        if (!context.hasReads() || !context.hasBasePileup() || (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) {
             counter.nUncovered = 1L;
             if (vcComp.getAttribute("GV").equals("T"))
                 counter.nAltNotCalled = 1L;