diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index cf528de09..1493815ee 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -730,7 +730,13 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
         if ( vc.getAlleles().size() != sub.getAlleles().size() )
             newGC = VariantContextUtils.stripPLs(sub.getGenotypes());
 
-        //Remove a fraction of the genotypes if needed
+        // if we have fewer samples in the selected VC than in the original VC, we need to strip out the MLE tags
+        if ( vc.getNSamples() != sub.getNSamples() ) {
+            builder.rmAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY);
+            builder.rmAttribute(VCFConstants.MLE_ALLELE_FREQUENCY_KEY);
+        }
+
+        // Remove a fraction of the genotypes if needed
         if ( fractionGenotypes > 0 ){
             ArrayList<Genotype> genotypes = new ArrayList<Genotype>();
             for ( Genotype genotype : newGC ) {
@@ -767,17 +773,21 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
 
         VariantContextUtils.calculateChromosomeCounts(builder, false);
 
+        boolean sawDP = false;
         int depth = 0;
         for (String sample : originalVC.getSampleNames()) {
             Genotype g = originalVC.getGenotype(sample);
 
             if ( ! g.isFiltered() ) {
-                if ( g.hasDP() )
+                if ( g.hasDP() ) {
                     depth += g.getDP();
+                    sawDP = true;
+                }
             }
         }
 
-        builder.attribute("DP", depth);
+        if ( sawDP )
+            builder.attribute("DP", depth);
     }
 
     private void randomlyAddVariant(int rank, VariantContext vc) {
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
index e25d65465..7a865ddeb 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -154,6 +154,32 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         executeTest("testRegenotype--" + testFile, spec);
     }
 
+    @Test
+    public void testRemoveMLE() {
+        String testFile = privateTestDir + "vcfexample.withMLE.vcf";
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
+                1,
+                Arrays.asList("")
+        );
+
+        executeTest("testRegenotype--" + testFile, spec);
+    }
+
+    @Test
+    public void testRemoveMLEAndRegenotype() {
+        String testFile = privateTestDir + "vcfexample.withMLE.vcf";
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
+                1,
+                Arrays.asList("")
+        );
+
+        executeTest("testRegenotype--" + testFile, spec);
+    }
+
     @Test
     public void testMultipleRecordsAtOnePosition() {
         String testFile = privateTestDir + "selectVariants.onePosition.vcf";