diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java
index 3a96b23e2..6a0d30837 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java
@@ -121,19 +121,23 @@ public class AlignmentContextUtils {
      * Splits the AlignmentContext into one context per read group
      *
      * @param context the original pileup
-     * @return a Map of ReadGroup to AlignmentContext
+     * @return a Map of ReadGroup to AlignmentContext, or an empty map if context has no base pileup
      *
      **/
     public static Map<SAMReadGroupRecord, AlignmentContext> splitContextByReadGroup(AlignmentContext context, Collection<SAMReadGroupRecord> readGroups) {
-        HashMap<SAMReadGroupRecord, AlignmentContext> contexts = new HashMap<SAMReadGroupRecord, AlignmentContext>();
+        if ( ! context.hasBasePileup() ) {
+            return Collections.emptyMap();
+        } else {
+            HashMap<SAMReadGroupRecord, AlignmentContext> contexts = new HashMap<SAMReadGroupRecord, AlignmentContext>();
 
-        for (SAMReadGroupRecord rg : readGroups) {
-            ReadBackedPileup rgPileup = context.getBasePileup().getPileupForReadGroup(rg.getReadGroupId());
-            if ( rgPileup != null ) // there we some reads for RG
-                contexts.put(rg, new AlignmentContext(context.getLocation(), rgPileup));
+            for (SAMReadGroupRecord rg : readGroups) {
+                ReadBackedPileup rgPileup = context.getBasePileup().getPileupForReadGroup(rg.getReadGroupId());
+                if ( rgPileup != null ) // there we some reads for RG
+                    contexts.put(rg, new AlignmentContext(context.getLocation(), rgPileup));
+            }
+
+            return contexts;
         }
-
-        return contexts;
     }
 
     public static Map<String, AlignmentContext> splitContextBySampleName(ReadBackedPileup pileup, String assumedSingleSample) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index a80508715..e60ace0cb 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -314,7 +314,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
                 genotypes.add(genotypePair.getValue());
         }
         
-        VariantContext sub = vc.subContextFromGenotypes(genotypes);
+        VariantContext sub = vc.subContextFromGenotypes(genotypes, vc.getAlleles());
 
         HashMap<String, Object> attributes = new HashMap<String, Object>(sub.getAttributes());
 
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
index 23fd43b01..66a7b4d9b 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -31,7 +31,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -sn A -sn B -sn C -B:variant,VCF3 " + testfile + " -NO_HEADER"),
                 1,
-                Arrays.asList("fe6963e5fea1d3854634dcf3defd7b92")
+                Arrays.asList("5ba7536a0819421b330350a160e4261a")
         );
 
         executeTest("testRepeatedLineSelection--" + testfile, spec);