diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java
index 827df16bb..eada8521f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java
@@ -27,11 +27,16 @@ package org.broadinstitute.sting.utils.codecs.snpEff;
 import org.broad.tribble.Feature;
 import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.TribbleException;
+import org.broad.tribble.readers.AsciiLineReader;
 import org.broad.tribble.readers.LineReader;
+import org.broadinstitute.sting.gatk.refdata.SelfScopingFeatureCodec;
+
 import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.EffectType;
 import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.ChangeType;
 import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.Zygosity;
 
+import java.io.File;
+import java.io.FileInputStream;
 import java.io.IOException;
 
 /**
@@ -68,7 +73,7 @@ import java.io.IOException;
  *
  * @author David Roazen
  */
-public class SnpEffCodec implements FeatureCodec {
+public class SnpEffCodec implements FeatureCodec, SelfScopingFeatureCodec {
 
     public static final int EXPECTED_NUMBER_OF_FIELDS = 23;
     public static final String FIELD_DELIMITER_PATTERN = "\\t";
@@ -255,4 +260,16 @@ public class SnpEffCodec implements FeatureCodec {
             }
         }
     }
+
+    public boolean canDecode ( final File potentialInput ) {
+        try {
+            LineReader reader = new AsciiLineReader(new FileInputStream(potentialInput));
+            readHeader(reader);
+        }
+        catch ( Exception e ) {
+            return false;
+        }
+
+        return true;
+    }
 }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
index 596ac5c36..af29bd01f 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -129,8 +129,8 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testSnpEffAnnotations() {
         WalkerTestSpec spec = new WalkerTestSpec(
-            "-T VariantAnnotator -R " + b37KGReference + " -NO_HEADER -o %s -A SnpEff --variant:VCF " +
-            validationDataLocation + "1000G.exomes.vcf --snpEffFile:SnpEff " + validationDataLocation +
+            "-T VariantAnnotator -R " + b37KGReference + " -NO_HEADER -o %s -A SnpEff --variant " +
+            validationDataLocation + "1000G.exomes.vcf --snpEffFile  " + validationDataLocation +
             "snpEff_1.9.6_1000G.exomes.vcf_hg37.61.out -L 1:26,000,000-26,500,000",
             1,
             Arrays.asList("c08648a078368c80530bff004b3157f1")