diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
index 9af334ff7..c1293b872 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -619,9 +619,9 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         String idFile = privateTestDir + "complexExample1.vcf.id";
 
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString(" -xlIDs " + idFile + " --variant " + testFile),
+                baseTestString(" -xlIDs " + idFile + " --variant " + testFile + " --forceValidOutput"),
                 1,
-                Arrays.asList("6c1e8591c134519bfc202b4ec7ef1f71")
+                Arrays.asList("45ad235b42bac75aa269e12bcd88a411")
         );
         spec.disableShadowBCF();
         executeTest("testExcludeSelectionID--" + testFile, spec);
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
index 7c32f3666..9559e066e 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
@@ -574,6 +574,9 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
     @Argument(fullName="ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES", required=false, doc="Allow samples other than those in the VCF to be specified on the command line. These samples will be ignored.")
     private boolean allowNonOverlappingCommandLineSamples = false;
 
+    @Argument(fullName="forceValidOutput", required=false, doc="Forces output VCF to be compliant to up to date version")
+    private boolean forceValidOutput = false;
+
     public enum NumberAlleleRestriction {
         ALL,
         BIALLELIC,
@@ -1008,7 +1011,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
      */
     private VariantContext subsetRecord(final VariantContext vc, final boolean preserveAlleles, final boolean removeUnusedAlternates) {
         //subContextFromSamples() always decodes the vc, which is a fairly expensive operation.  Avoid if possible
-        if ( noSamplesSpecified && !removeUnusedAlternates )
+        if ( noSamplesSpecified && !removeUnusedAlternates && !forceValidOutput )
             return vc;
 
         // strip out the alternate alleles that aren't being used