diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
index 330d29c79..301baaba3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -36,10 +36,10 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
 import org.broadinstitute.sting.utils.help.HelpConstants;
+import org.broadinstitute.sting.utils.help.HelpUtils;
 import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.variant.variantcontext.VariantContext;
@@ -47,7 +47,6 @@ import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 
 import java.util.*;
 
-
 /**
  * Annotates variant calls with context information.
  *
@@ -165,7 +164,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
     protected Boolean USE_ALL_ANNOTATIONS = false;
 
     /**
-     * Note that the --list argument requires a fully resolved and correct command-line to work.
+     * Note that the --list argument requires a fully resolved and correct command-line to work. As a simpler alternative, you can use ListAnnotations (see Help Utilities).
      */
     @Argument(fullName="list", shortName="ls", doc="List the available annotations and exit", required=false)
     protected Boolean LIST = false;
@@ -177,7 +176,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
     protected Boolean ALWAYS_APPEND_DBSNP_ID = false;
     public boolean alwaysAppendDbsnpId() { return ALWAYS_APPEND_DBSNP_ID; }
 
-    @Argument(fullName="MendelViolationGenotypeQualityThreshold",shortName="mvq",required=false,doc="The genotype quality treshold in order to annotate mendelian violation ratio")
+    @Argument(fullName="MendelViolationGenotypeQualityThreshold",shortName="mvq",required=false,doc="The genotype quality threshold in order to annotate mendelian violation ratio")
     public double minGenotypeQualityP = 0.0;
 
     @Argument(fullName="requireStrictAlleleMatch", shortName="strict", doc="If provided only comp tracks that exactly match both reference and alternate alleles will be counted as concordant", required=false)
@@ -185,33 +184,14 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
 
     private VariantAnnotatorEngine engine;
 
-
-    private void listAnnotationsAndExit() {
-        System.out.println("\nStandard annotations in the list below are marked with a '*'.");
-        List<Class<? extends InfoFieldAnnotation>> infoAnnotationClasses = new PluginManager<InfoFieldAnnotation>(InfoFieldAnnotation.class).getPlugins();
-        System.out.println("\nAvailable annotations for the VCF INFO field:");
-        for (int i = 0; i < infoAnnotationClasses.size(); i++)
-            System.out.println("\t" + (StandardAnnotation.class.isAssignableFrom(infoAnnotationClasses.get(i)) ? "*" : "") + infoAnnotationClasses.get(i).getSimpleName());
-        System.out.println();
-        List<Class<? extends GenotypeAnnotation>> genotypeAnnotationClasses = new PluginManager<GenotypeAnnotation>(GenotypeAnnotation.class).getPlugins();
-        System.out.println("\nAvailable annotations for the VCF FORMAT field:");
-        for (int i = 0; i < genotypeAnnotationClasses.size(); i++)
-            System.out.println("\t" + (StandardAnnotation.class.isAssignableFrom(genotypeAnnotationClasses.get(i)) ? "*" : "") + genotypeAnnotationClasses.get(i).getSimpleName());
-        System.out.println();
-        System.out.println("\nAvailable classes/groups of annotations:");
-        for ( Class c : new PluginManager<AnnotationType>(AnnotationType.class).getInterfaces() )
-            System.out.println("\t" + c.getSimpleName());
-        System.out.println();
-        System.exit(0);
-    }
-
     /**
      * Prepare the output file and the list of available features.
      */
     public void initialize() {
 
         if ( LIST )
-            listAnnotationsAndExit();
+            HelpUtils.listAnnotations();
+            System.exit(0);
 
         // get the list of all sample names from the variant VCF input rod, if applicable
         List<String> rodName = Arrays.asList(variantCollection.variants.getName());
diff --git a/public/java/src/org/broadinstitute/sting/tools/CatVariants.java b/public/java/src/org/broadinstitute/sting/tools/CatVariants.java
index e1dd2c255..ad77b2548 100644
--- a/public/java/src/org/broadinstitute/sting/tools/CatVariants.java
+++ b/public/java/src/org/broadinstitute/sting/tools/CatVariants.java
@@ -35,7 +35,6 @@ import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.help.HelpConstants;
 import org.broadinstitute.variant.bcf2.BCF2Codec;
@@ -54,7 +53,7 @@ import java.util.*;
 
 /**
  *
- * Concatenates VCF files of non-overlapped genome intervals, all with the same set of samples.
+ * Concatenates VCF files of non-overlapped genome intervals, all with the same set of samples
  *
  * <p>
  * The main purpose of this tool is to speed up the gather function when using scatter-gather parallelization.
@@ -80,10 +79,14 @@ import java.util.*;
  * A combined VCF. The output file should be 'name.vcf' or 'name.VCF'.
  * <\p>
  *
+ * <h3>Important note</h3>
+ * <p>This is a command-line utility that bypasses the GATK engine. As a result, the command-line you must use to
+ * invoke it is a little different from other GATK tools (see example below), and it does not accept any of the
+ * classic "CommandLineGATK" arguments.</p>
  *
- * <h3>Examples</h3>
+ * <h3>Example</h3>
  * <pre>
- * java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.CatVariants \
+ * java -cp GenomeAnalysisTK.jar org.broadinstitute.sting.tools.CatVariants \
  *    -R ref.fasta \
  *    -V input1.vcf \
  *    -V input2.vcf \
@@ -95,7 +98,7 @@ import java.util.*;
  * @since Jan 2012
  */
 
-@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP )
 public class CatVariants extends CommandLineProgram {
     // setup the logging system, used by some codecs
     private static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getRootLogger();
@@ -124,7 +127,7 @@ public class CatVariants extends CommandLineProgram {
      * print usage information
      */
     private static void printUsage() {
-        System.err.println("Usage: java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.AppendVariants <reference> <input VCF or BCF files> <outputFile> [sorted (optional)]");
+        System.err.println("Usage: java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.CatVariants <reference> <input VCF or BCF files> <outputFile> [sorted (optional)]");
         System.err.println("    The input files can be of type: VCF (ends in .vcf or .VCF)");
         System.err.println("                                    BCF2 (ends in .bcf or .BCF)");
         System.err.println("    Output file must be vcf or bcf file (.vcf or .bcf)");
diff --git a/public/java/src/org/broadinstitute/sting/tools/ListAnnotations.java b/public/java/src/org/broadinstitute/sting/tools/ListAnnotations.java
new file mode 100644
index 000000000..fabcf828a
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/tools/ListAnnotations.java
@@ -0,0 +1,85 @@
+/*
+* Copyright (c) 2012 The Broad Institute
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.sting.tools;
+
+import org.broadinstitute.sting.commandline.CommandLineProgram;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.sting.utils.help.HelpConstants;
+import org.broadinstitute.sting.utils.help.HelpUtils;
+
+/**
+ * Utility program to print a list of available annotations
+ *
+ * <p>This is a very simple utility tool that retrieves available annotations for use with tools such as
+ * UnifiedGenotyper, HaplotypeCaller and VariantAnnotator.</p>
+ *
+ * <h3>Important note</h3>
+ * <p>This is a command-line utility that bypasses the GATK engine. As a result, the command-line you must use to
+ * invoke it is a little different from other GATK tools (see usage below), and it does not accept any of the
+ * classic "CommandLineGATK" arguments.</p>
+ *
+ * <h3>Usage</h3>
+ * <pre>java -cp GenomeAnalysisTK.jar org.broadinstitute.sting.tools.ListAnnotations</pre>
+ *
+ * @author vdauwera
+ * @since 3/14/13
+ */
+@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_HELPUTILS )
+public class ListAnnotations extends CommandLineProgram {
+
+    /*
+     * Print usage information
+     *
+     * TODO: would be more convenient if we could just call the program by name instead of the full classpath
+     */
+    private static void printUsage() {
+        System.err.println("Usage: java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.ListAnnotations");
+        System.err.println("    Prints a list of available annotations and exits.");
+    }
+
+    // TODO: override CommandLineProgram bit that offers version, logging etc arguments. We don't need that stuff here and it makes the doc confusing.
+
+    @Override
+    protected int execute() throws Exception {
+
+        HelpUtils.listAnnotations();
+        return 0;
+    }
+
+    public static void main(String[] args){
+        try {
+            ListAnnotations instance = new ListAnnotations();
+            start(instance, args);
+            System.exit(CommandLineProgram.result);
+        } catch ( UserException e ) {
+            printUsage();
+            exitSystemWithUserError(e);
+        } catch ( Exception e ) {
+            exitSystemWithError(e);
+        }
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/HelpConstants.java b/public/java/src/org/broadinstitute/sting/utils/help/HelpConstants.java
index f99ff7538..2ed35d848 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/HelpConstants.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/HelpConstants.java
@@ -56,6 +56,7 @@ public class HelpConstants {
     public final static String DOCS_CAT_VARDISC = "Variant Discovery Tools";
     public final static String DOCS_CAT_VARMANIP = "Variant Evaluation and Manipulation Tools";
     public final static String DOCS_CAT_TEST = "Testing Tools";
+    public final static String DOCS_CAT_HELPUTILS = "Help Utilities";
 
     public static String forumPost(String post) {
     	return GATK_FORUM_URL + post;
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java b/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java
index 81606d2f3..9a23fd022 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java
@@ -28,9 +28,15 @@ package org.broadinstitute.sting.utils.help;
 import com.sun.javadoc.FieldDoc;
 import com.sun.javadoc.PackageDoc;
 import com.sun.javadoc.ProgramElementDoc;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.broadinstitute.sting.utils.classloader.PluginManager;
 
 import java.lang.reflect.Field;
+import java.util.List;
 
 public class HelpUtils {
 
@@ -70,4 +76,27 @@ public class HelpUtils {
                 String.format("%s", doc.name());
     }
 
+    /**
+     * Simple method to print a list of available annotations.
+     */
+    public static void listAnnotations() {
+        System.out.println("\nThis is a list of available Variant Annotations for use with tools such as UnifiedGenotyper, HaplotypeCaller and VariantAnnotator. Please see the Technical Documentation for more details about these annotations:");
+        System.out.println("http://www.broadinstitute.org/gatk/gatkdocs/");
+        System.out.println("\nStandard annotations in the list below are marked with a '*'.");
+        List<Class<? extends InfoFieldAnnotation>> infoAnnotationClasses = new PluginManager<InfoFieldAnnotation>(InfoFieldAnnotation.class).getPlugins();
+        System.out.println("\nAvailable annotations for the VCF INFO field:");
+        for (int i = 0; i < infoAnnotationClasses.size(); i++)
+            System.out.println("\t" + (StandardAnnotation.class.isAssignableFrom(infoAnnotationClasses.get(i)) ? "*" : "") + infoAnnotationClasses.get(i).getSimpleName());
+        System.out.println();
+        List<Class<? extends GenotypeAnnotation>> genotypeAnnotationClasses = new PluginManager<GenotypeAnnotation>(GenotypeAnnotation.class).getPlugins();
+        System.out.println("\nAvailable annotations for the VCF FORMAT field:");
+        for (int i = 0; i < genotypeAnnotationClasses.size(); i++)
+            System.out.println("\t" + (StandardAnnotation.class.isAssignableFrom(genotypeAnnotationClasses.get(i)) ? "*" : "") + genotypeAnnotationClasses.get(i).getSimpleName());
+        System.out.println();
+        System.out.println("\nAvailable classes/groups of annotations:");
+        for ( Class c : new PluginManager<AnnotationType>(AnnotationType.class).getInterfaces() )
+            System.out.println("\t" + c.getSimpleName());
+        System.out.println();
+    }
+
 }
\ No newline at end of file