diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
index 0dc1dad07..c74f72210 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
@@ -163,7 +163,6 @@ public class SequenomValidationConverter extends RodWalker<Pair<VariantContext,
 
         for ( Pair<VariantContext, Byte> record : records )
             vcfwriter.add(record.first, record.second);
-        vcfwriter.close();
     }
 
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
index e1f4b7e04..dcc413a19 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
@@ -65,9 +65,9 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
     @Output(doc="File to which variants should be written",required=true)
     protected VCFWriter vcfWriter = null;
 
-    @Argument(fullName="output_file", shortName="output", doc="Please use --out instead")
+    @Argument(fullName="output_file", shortName="output", doc="Please use --out instead" ,required=false)
     @Deprecated
-    private String oldOutputArg;
+    protected String oldOutputArg;
 
     @Argument(fullName="no" +
             "call_threshold", shortName="ncthr", doc="Threshold of confidence at which a genotype won't be called", required=false)
diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java
index 3b0758da2..e6e0ead0d 100755
--- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java
@@ -41,7 +41,7 @@ public class BeagleIntegrationTest extends WalkerTest {
                         "-B beagleR2,BEAGLE," + beagleValidationDataLocation + "inttestbgl.r2 " +
                         "-B beagleProbs,BEAGLE," + beagleValidationDataLocation + "inttestbgl.gprobs " +
                         "-B beaglePhased,BEAGLE," + beagleValidationDataLocation + "inttestbgl.phased " +
-                        "-output %s", 1, Arrays.asList("e7b9aac20246f26ffcc599850f6cb2a0"));
+                        "-o %s", 1, Arrays.asList("e7b9aac20246f26ffcc599850f6cb2a0"));
         executeTest("test BeagleOutputToVCF", spec);
     }