diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
index 343e6c96c..bdd4ed2ec 100755
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
 
 import com.google.java.contract.Ensures;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
@@ -99,6 +100,7 @@ import java.util.*;
  * @since 8/22/11
  */
 
+@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
 @PartitionBy(PartitionType.LOCUS)
 @ActiveRegionExtension(extension=65, maxRegion=275)
 public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implements AnnotatorCompatible {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java
index fb265d4e0..13821420c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java
@@ -42,6 +42,7 @@ import org.broadinstitute.sting.utils.clipping.ClippingOp;
 import org.broadinstitute.sting.utils.clipping.ClippingRepresentation;
 import org.broadinstitute.sting.utils.clipping.ReadClipper;
 import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.io.File;
@@ -148,6 +149,7 @@ import java.util.regex.Pattern;
  * @author Mark DePristo
  * @since 2010
  */
+@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools" )
 @Requires({DataSource.READS})
 public class ClipReads extends ReadWalker<ClipReads.ReadClipperWithData, ClipReads.ClippingData> {
     /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java
index 6e9960f3a..e33ad16fd 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java
@@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.io.File;
@@ -88,6 +89,7 @@ import java.util.TreeSet;
  * </pre>
  *
  */
+@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools" )
 @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT)
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
index 263320d1b..8d395422a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
@@ -9,6 +9,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Arrays;
@@ -20,6 +21,7 @@ import java.util.Map;
 /**
  * The GC content (# GC bases / # all bases) of the reference within 50 bp +/- this site
  */
+@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools" )
 public class GCContent extends InfoFieldAnnotation implements ExperimentalAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
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 d6d2beb91..07587743e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 
@@ -75,6 +76,7 @@ import java.util.*;
  * </pre>
  *
  */
+@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
 @Requires(value={})
 @Allows(value={DataSource.READS, DataSource.REFERENCE})
 @Reference(window=@Window(start=-50,stop=50))
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java
index 627d561f6..8e9936540 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java
@@ -36,6 +36,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.*;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 
@@ -72,6 +73,7 @@ import static java.lang.Math.log10;
  <p> Note that Beagle produces some of these files compressed as .gz, so gunzip must be run on them before walker is run in order to decompress them </p>
 
  */
+@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
 public class BeagleOutputToVCF extends RodWalker<Integer, Integer> {
 
     @ArgumentCollection
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
index 14e92a066..d0570d52f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
@@ -42,6 +42,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.*;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 
@@ -75,6 +76,7 @@ import java.util.*;
  *
  */
 
+@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
 public class ProduceBeagleInput extends RodWalker<Integer, Integer> {
 
     @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
index 4cba67909..1afa7dc35 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
@@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.recalibration.RecalibrationTables;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@@ -97,13 +98,12 @@ import java.util.ArrayList;
  * </pre>
  */
 
+@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools" )
 @BAQMode(ApplicationTime = BAQ.ApplicationTime.FORBIDDEN)
 @By(DataSource.READS)
-
 @ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class})                                   // only look at covered loci, not every loci of the reference file
 @Requires({DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES})                                         // filter out all reads with zero or unavailable mapping quality
 @PartitionBy(PartitionType.LOCUS)                                                                                       // this walker requires both -I input.bam and -R reference.fasta
-
 public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeReducible<Long> {
     @ArgumentCollection
     private final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();                          // all the command line arguments for BQSR and it's covariates
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
index bc791a5a4..ebd5774b4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
@@ -35,6 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 
 import java.io.File;
@@ -119,6 +120,7 @@ import java.io.PrintStream;
  * @author Mark DePristo
  * @since May 7, 2010
  */
+@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools" )
 @By(DataSource.REFERENCE)
 public class CallableLoci extends LocusWalker<CallableLoci.CallableBaseState, CallableLoci.Integrator> {
     @Output
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
index 9fc1ec2f3..90dbfd317 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
@@ -48,6 +48,7 @@ import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 
 import java.io.File;
 import java.io.PrintStream;
@@ -114,6 +115,7 @@ import java.util.*;
 // todo -- alter logarithmic scaling to spread out bins more
 // todo -- allow for user to set linear binning (default is logarithmic)
 // todo -- formatting --> do something special for end bins in getQuantile(int[] foo), this gets mushed into the end+-1 bins for now
+@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools" )
 @By(DataSource.REFERENCE)
 @PartitionBy(PartitionType.NONE)
 @Downsample(by= DownsampleType.NONE, toCoverage=Integer.MAX_VALUE)
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java
index e4e3c271e..c123a3828 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java
@@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.report.GATKReport;
 import org.broadinstitute.sting.gatk.report.GATKReportTable;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.Median;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.io.PrintStream;
@@ -94,6 +95,7 @@ import java.util.Map;
  *
  * @author Mark DePristo
  */
+@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools" )
 public class ReadGroupProperties extends ReadWalker<Integer, Integer> {
     @Output
     public PrintStream out;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java
index 0d390308e..8650df8bd 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java
@@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Collections;
@@ -70,6 +71,7 @@ import java.util.List;
  * </pre>
  *
  */
+@DocumentedGATKFeature( groupName = "Companion Utilities" )
 @WalkerName("FastaAlternateReferenceMaker")
 @Reference(window=@Window(start=-1,stop=50))
 @Requires(value={DataSource.REFERENCE})
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java
index f1eb6d028..afac6de97 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java
@@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.walkers.RefWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 
 import java.io.PrintStream;
 
@@ -66,6 +67,7 @@ import java.io.PrintStream;
  * </pre>
  *
  */
+@DocumentedGATKFeature( groupName = "Companion Utilities" )
 @WalkerName("FastaReferenceMaker")
 public class FastaReference extends RefWalker<Pair<GenomeLoc, String>, GenomeLoc> {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
index 1415239b4..6b01c563a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
@@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.*;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 
@@ -75,6 +76,7 @@ import java.util.*;
  * </pre>
  *
  */
+@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
 @Reference(window=@Window(start=-50,stop=50))
 public class VariantFiltration extends RodWalker<Integer, Integer> {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index b3a0b2a5d..35dacbdd6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -41,6 +41,7 @@ import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
@@ -114,6 +115,7 @@ import java.util.*;
  *
  */
 
+@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
 @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_INPUT)
 @ReadFilters( {BadMateFilter.class, MappingQualityUnavailableFilter.class} )
 @Reference(window=@Window(start=-200,stop=200))
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index addfc5fab..c1b784801 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -46,6 +46,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.NWaySAMFileWriter;
@@ -109,6 +110,7 @@ import java.util.*;
  *
  * @author ebanks
  */
+@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools" )
 @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT)
 public class IndelRealigner extends ReadWalker<Integer, Integer> {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
index 5f39f4ea8..d916711b5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
@@ -37,6 +37,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -94,6 +95,7 @@ import java.util.TreeSet;
  *
  * @author ebanks
  */
+@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools" )
 @ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class, BadMateFilter.class, Platform454Filter.class, BadCigarFilter.class})
 @Reference(window=@Window(start=-1,stop=50))
 @Allows(value={DataSource.READS, DataSource.REFERENCE})
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
index 21db1412b..743dd3e26 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
@@ -57,6 +57,7 @@ import org.broadinstitute.sting.utils.collections.CircularArray;
 import org.broadinstitute.sting.utils.collections.PrimitivePair;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
 import org.broadinstitute.sting.utils.interval.OverlappingIntervalIterator;
@@ -126,6 +127,7 @@ import java.util.*;
  *
  */
 
+@DocumentedGATKFeature( groupName = "Cancer-specific Variant Discovery Tools" )
 @ReadFilters({Platform454Filter.class, MappingQualityZeroFilter.class, PlatformUnitFilter.class})
 public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
 //    @Output
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
index 4760893ca..fe30d2d9e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
@@ -12,6 +12,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.*;
@@ -72,6 +73,7 @@ import java.util.*;
  * </pre>
  *
  */
+@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
 public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMap<Byte,Integer>> {
 
     @ArgumentCollection
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
index 154c8c789..1aabf6356 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
@@ -40,6 +40,7 @@ import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.variantcontext.*;
@@ -91,6 +92,7 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
 // Filter out all reads with zero mapping quality
 @ReadFilters({MappingQualityZeroFilter.class})
 
+@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
 public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingStats> {
     private static final boolean DEBUG = false;
     /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java
index 11cf0fe39..f70d1292c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java
@@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 
 import java.io.PrintStream;
 
@@ -37,6 +38,7 @@ import java.io.PrintStream;
  * </pre>
  *
  */
+@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools" )
 public class CountLoci extends LocusWalker<Integer, Long> implements TreeReducible<Long> {
     @Output(doc="Write count to this file instead of STDOUT")
     PrintStream out;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java
index c9108054e..979edefda 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java
@@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 /**
@@ -36,6 +37,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
  * </pre>
  *
  */
+@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools" )
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class CountReads extends ReadWalker<Integer, Integer> {
     public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
index 3d008de43..3d3feab4e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
@@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
@@ -188,13 +189,11 @@ import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel;
  * @since ${DATE}
  */
 
+@DocumentedGATKFeature( groupName = "Validation Utilities" )
 @Requires(value={DataSource.READS, DataSource.REFERENCE})
 @Allows(value={DataSource.READS, DataSource.REFERENCE})
-
 @By(DataSource.REFERENCE)
 @Reference(window=@Window(start=-200,stop=200))
-
-
 public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedData, GenotypeAndValidate.CountedData> implements TreeReducible<GenotypeAndValidate.CountedData> {
 
     /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
index 3d281ef6c..705acb606 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
@@ -18,6 +18,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
@@ -88,6 +89,7 @@ import java.util.List;
  * @author chartl
  * @since July 2011
  */
+@DocumentedGATKFeature( groupName = "Validation Utilities" )
 @Requires(value={DataSource.REFERENCE})
 public class ValidationAmplicons extends RodWalker<Integer,Integer> {
     /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java
index cdcac2300..0c4dcb57d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java
@@ -33,6 +33,7 @@ import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
@@ -96,6 +97,7 @@ import java.util.*;
  * </pre>
  *
  */
+@DocumentedGATKFeature( groupName = "Validation Utilities" )
 public class ValidationSiteSelector extends RodWalker<Integer, Integer> {
 
     public enum AF_COMPUTATION_MODE {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
index 1b5474777..1e1704f96 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
@@ -26,6 +26,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
@@ -86,6 +87,7 @@ import java.util.*;
  * </pre>
  *
  */
+@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
 @Reference(window=@Window(start=-50, stop=50))
 @PartitionBy(PartitionType.NONE)
 public class VariantEval extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
index 0dfdd4ba1..44ffcb3a9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
@@ -38,6 +38,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -85,6 +86,7 @@ import java.util.*;
  *
  */
 
+@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
 @PartitionBy(PartitionType.LOCUS)
 public class ApplyRecalibration extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 244c5d109..9c5237322 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -42,6 +42,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.io.Resource;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
@@ -109,6 +110,7 @@ import java.util.*;
  *
  */
 
+@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
 @PartitionBy(PartitionType.NONE)
 public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDatum>, ExpandingArrayList<VariantDatum>> implements TreeReducible<ExpandingArrayList<VariantDatum>> {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index 94fa29173..555670870 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
@@ -96,6 +97,7 @@ import java.util.*;
  * </pre>
  *
  */
+@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
 @Reference(window=@Window(start=-50,stop=50))
 public class CombineVariants extends RodWalker<Integer, Integer> {
     /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
index c1755aa00..eee0f33dc 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
@@ -41,6 +41,7 @@ import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.variantcontext.*;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
@@ -76,6 +77,7 @@ import java.util.*;
  * </pre>
  *
  */
+@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
 @Reference(window=@Window(start=-200,stop=200))
 public class LeftAlignVariants extends RodWalker<Integer, Integer> {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index fbffd620a..cd25cc22d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -41,6 +41,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
 import org.broadinstitute.sting.utils.MendelianViolation;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
@@ -186,6 +187,7 @@ import java.util.*;
  * </pre>
  *
  */
+@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
 public class SelectVariants extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
     @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
index 530258fe0..3132db3e8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
@@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
@@ -66,6 +67,7 @@ import java.util.Set;
  * </pre>
  *
  */
+@DocumentedGATKFeature( groupName = "Validation Utilities" )
 @Reference(window=@Window(start=0,stop=100))
 public class ValidateVariants extends RodWalker<Integer, Integer> {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
index 3fca2d28a..66a737269 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
@@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -81,6 +82,7 @@ import java.util.*;
  * </pre>
  *
  */
+@DocumentedGATKFeature( groupName = "Validation Utilities" )
 @Reference(window=@Window(start=0,stop=40))
 public class VariantValidationAssessor extends RodWalker<VariantContext,Integer> {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
index 996ac75e7..a6f8bc3aa 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
@@ -29,6 +29,7 @@ import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -97,6 +98,7 @@ import java.util.*;
  * @author Mark DePristo
  * @since 2010
  */
+@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
 public class VariantsToTable extends RodWalker<Integer, Integer> {
     /**
      * Variants from this VCF file are used by this tool as input.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
index e8c6794f2..411527947 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
@@ -44,6 +44,7 @@ import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.*;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
@@ -78,6 +79,7 @@ import java.util.*;
  * </pre>
  *
  */
+@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
 @Reference(window=@Window(start=-40,stop=40))
 public class VariantsToVCF extends RodWalker<Integer, Integer> {