diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 758d52e68..d16ece4fd 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -176,7 +176,7 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
     /**
      * A raw, unfiltered, highly sensitive callset in VCF format.
      */
-    @Gather(className = "org.broadinstitute.sting.queue.extensions.gatk.CatVariantsGatherer")
+    //@Gather(className = "org.broadinstitute.sting.queue.extensions.gatk.CatVariantsGatherer")
     @Output(doc="File to which variants should be written",required=true)
     protected VariantContextWriter writer = null;
 
diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
index 1bf4c69fc..51cc576aa 100644
--- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
+++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
@@ -158,12 +158,18 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
             List<ArgumentField> fields = new ArrayList<ArgumentField>();
 
             String gatherClass;
+
+            // one can set the specific gatherer to use by adding @Gather before any output argument.
+            // For example (used to be part of UG):
+            //      @Gather(className = "org.broadinstitute.sting.queue.extensions.gatk.CatVariantsGatherer")
+            //      @Output(doc="File to which variants should be written",required=true)
+            //      protected VariantContextWriter writer = null;
             if (gatherer != null)
                 gatherClass = gatherer;
             else if (SAMFileWriter.class.isAssignableFrom(argumentDefinition.argumentType))
                 gatherClass = "BamGatherFunction";
             else if (VariantContextWriter.class.isAssignableFrom(argumentDefinition.argumentType))
-                gatherClass = "VcfGatherFunction";
+                gatherClass = "CatVariantsGatherer"; // used to be "VcfGatherFunction";
             else
                 gatherClass = "org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction";
 
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala
index 848554dfc..30fd4c81f 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala
@@ -30,11 +30,13 @@ import org.broadinstitute.sting.queue.function.scattergather.GatherFunction
 
 
 /**
- * Created with IntelliJ IDEA.
- * User: ami
- * Date: 12/11/12
- * Time: 2:04 PM
- * To change this template use File | Settings | File Templates.
+ *
+ * Currently this is the default gather for VCFs.
+ * One can set a specific gatherer to use by adding @Gather before any output argument.
+ * For example (used to be part of UG):
+ *           @Gather(className = "org.broadinstitute.sting.queue.extensions.gatk.CatVariantsGatherer")
+ *           @Output(doc="File to which variants should be written",required=true)
+ *           protected VariantContextWriter writer = null;
  */
 class CatVariantsGatherer extends CatVariants with GatherFunction with RetryMemoryLimit{
   this.assumeSorted = true
@@ -45,6 +47,7 @@ class CatVariantsGatherer extends CatVariants with GatherFunction with RetryMemo
     this.reference = originalGATK.reference_sequence
     this.variant = this.gatherParts.zipWithIndex map { case (input, index) => new TaggedFile(input, "input"+index) }
     this.outputFile = this.originalOutput
+    this.assumeSorted = true
     super.freezeFieldValues()
   }