diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java
index 845c65c9c..85f7cc078 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java
@@ -410,6 +410,12 @@ public class GenotypesContext implements List<Genotype> {
         return getGenotypes().get(i);
     }
 
+    /**
+     * Gets sample associated with this sampleName, or null if none is found
+     *
+     * @param sampleName
+     * @return
+     */
     public Genotype get(final String sampleName) {
         Integer offset = getSampleI(sampleName);
         return offset == null ? null : getGenotypes().get(offset);
@@ -648,16 +654,15 @@ public class GenotypesContext implements List<Genotype> {
     @Ensures("result != null")
     public GenotypesContext subsetToSamples( final Set<String> samples ) {
         final int nSamples = samples.size();
-        final int nGenotypes = size();
 
-        if ( nSamples == nGenotypes )
-            return this;
-        else if ( nSamples == 0 )
+        if ( nSamples == 0 )
             return NO_GENOTYPES;
         else { // nGenotypes < nSamples
             final GenotypesContext subset = create(samples.size());
             for ( final String sample : samples ) {
-                subset.add(get(sample));
+                final Genotype g = get(sample);
+                if ( g != null )
+                    subset.add(g);
             }
             return subset;
         }
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
index fca7440e4..0e75eee14 100755
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
@@ -704,11 +704,14 @@ public class VariantContextUnitTest extends BaseTest {
     public Object[][] MakeSubContextTest() {
         for ( boolean updateAlleles : Arrays.asList(true, false)) {
             new SubContextTest(Collections.<String>emptySet(), updateAlleles);
+            new SubContextTest(Collections.singleton("MISSING"), updateAlleles);
             new SubContextTest(Collections.singleton("AA"), updateAlleles);
             new SubContextTest(Collections.singleton("AT"), updateAlleles);
             new SubContextTest(Collections.singleton("TT"), updateAlleles);
             new SubContextTest(Arrays.asList("AA", "AT"), updateAlleles);
             new SubContextTest(Arrays.asList("AA", "AT", "TT"), updateAlleles);
+            new SubContextTest(Arrays.asList("AA", "AT", "MISSING"), updateAlleles);
+            new SubContextTest(Arrays.asList("AA", "AT", "TT", "MISSING"), updateAlleles);
         }
 
         return SubContextTest.getTests(SubContextTest.class);