diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
index d793ae159..189575d6f 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
@@ -32,6 +32,7 @@ import net.sf.samtools.util.SequenceUtil;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.filters.*;
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 bdd4ed2ec..f5f707690 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
@@ -29,6 +29,7 @@ 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.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -100,7 +101,7 @@ import java.util.*;
  * @since 8/22/11
  */
 
-@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
+@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
 @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 13821420c..beafd0870 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java
@@ -33,6 +33,7 @@ import org.broadinstitute.sting.commandline.Advanced;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
@@ -149,7 +150,7 @@ import java.util.regex.Pattern;
  * @author Mark DePristo
  * @since 2010
  */
-@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools" )
+@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
 @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 e33ad16fd..8257794d7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java
@@ -29,6 +29,7 @@ import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMReadGroupRecord;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
@@ -89,7 +90,7 @@ import java.util.TreeSet;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools" )
+@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
 @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 8d395422a..fba30b3f7 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
@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -21,7 +22,7 @@ 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" )
+@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
 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 07587743e..cce106210 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
@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
 import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -76,7 +77,7 @@ import java.util.*;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
+@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
 @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 8e9936540..0aa05cf89 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
@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.walkers.beagle;
 
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -73,7 +74,7 @@ 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" )
+@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
 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 d0570d52f..0224d76a4 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
@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.walkers.beagle;
 
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -76,7 +77,7 @@ import java.util.*;
  *
  */
 
-@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
+@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
 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 1afa7dc35..b2400a49d 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
@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.bqsr;
 
 import net.sf.samtools.SAMFileHeader;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter;
@@ -98,7 +99,7 @@ import java.util.ArrayList;
  * </pre>
  */
 
-@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools" )
+@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
 @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
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 ebd5774b4..58ddd0879 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
@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.coverage;
 import org.broadinstitute.sting.commandline.Advanced;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -120,7 +121,7 @@ import java.io.PrintStream;
  * @author Mark DePristo
  * @since May 7, 2010
  */
-@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools" )
+@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
 @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 90dbfd317..c5b043b7a 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
@@ -29,6 +29,7 @@ import net.sf.samtools.SAMReadGroupRecord;
 import org.broadinstitute.sting.commandline.Advanced;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.DownsampleType;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -115,7 +116,7 @@ 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" )
+@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
 @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 c123a3828..9289f86e3 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
@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics;
 import net.sf.samtools.SAMReadGroupRecord;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.report.GATKReport;
@@ -95,7 +96,7 @@ import java.util.Map;
  *
  * @author Mark DePristo
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools" )
+@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
 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 8650df8bd..9c9a75fc4 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
@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.fasta;
 
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.RodBinding;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -71,7 +72,7 @@ import java.util.List;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Companion Utilities" )
+@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} )
 @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 afac6de97..a835560d4 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
@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.fasta;
 
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -67,7 +68,7 @@ import java.io.PrintStream;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Companion Utilities" )
+@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} )
 @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 6b01c563a..8b3886cfb 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
@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.filters;
 
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -76,7 +77,7 @@ import java.util.*;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
+@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
 @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 35dacbdd6..cd1815d82 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
@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.DownsampleType;
 import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -115,7 +116,7 @@ import java.util.*;
  *
  */
 
-@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
+@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
 @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 c1b784801..2153525ab 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
@@ -32,6 +32,7 @@ import net.sf.samtools.util.SequenceUtil;
 import net.sf.samtools.util.StringUtil;
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
@@ -110,7 +111,7 @@ import java.util.*;
  *
  * @author ebanks
  */
-@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools" )
+@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
 @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 d916711b5..02e4d414d 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
@@ -29,6 +29,7 @@ import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.commandline.RodBinding;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.filters.*;
@@ -95,7 +96,7 @@ import java.util.TreeSet;
  *
  * @author ebanks
  */
-@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools" )
+@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
 @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 743dd3e26..0fd047f58 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
@@ -32,6 +32,7 @@ import org.apache.commons.jexl2.JexlEngine;
 import org.apache.commons.jexl2.MapContext;
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
 import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
@@ -127,7 +128,7 @@ import java.util.*;
  *
  */
 
-@DocumentedGATKFeature( groupName = "Cancer-specific Variant Discovery Tools" )
+@DocumentedGATKFeature( groupName = "Cancer-specific Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
 @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 fe30d2d9e..3cf1d485e 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
@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.phasing;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -73,7 +74,7 @@ import java.util.*;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
+@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
 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 1aabf6356..f16deb701 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
@@ -27,6 +27,7 @@ import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -92,7 +93,7 @@ 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" )
+@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
 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 f70d1292c..bd10eab87 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
@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.qc;
 
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -38,7 +39,7 @@ import java.io.PrintStream;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools" )
+@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
 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 979edefda..5a9e5e7d2 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
@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.qc;
 
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
@@ -37,7 +38,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools" )
+@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
 @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 3d3feab4e..5beeeb3e6 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
@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.walkers.validation;
 
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -189,7 +190,7 @@ import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel;
  * @since ${DATE}
  */
 
-@DocumentedGATKFeature( groupName = "Validation Utilities" )
+@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
 @Requires(value={DataSource.READS, DataSource.REFERENCE})
 @Allows(value={DataSource.READS, DataSource.REFERENCE})
 @By(DataSource.REFERENCE)
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 705acb606..9676704c2 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
@@ -8,6 +8,7 @@ import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.BWTFiles;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -89,7 +90,7 @@ import java.util.List;
  * @author chartl
  * @since July 2011
  */
-@DocumentedGATKFeature( groupName = "Validation Utilities" )
+@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
 @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 0c4dcb57d..9e5fd25a9 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
@@ -24,6 +24,7 @@
 package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector;
 
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -97,7 +98,7 @@ import java.util.*;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Validation Utilities" )
+@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
 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 1e1704f96..0b395bc62 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
@@ -7,6 +7,7 @@ import net.sf.samtools.SAMSequenceRecord;
 import org.apache.log4j.Logger;
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -87,7 +88,7 @@ import java.util.*;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
+@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
 @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 44ffcb3a9..744a094c6 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
@@ -29,6 +29,7 @@ import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.commandline.RodBinding;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -86,7 +87,7 @@ import java.util.*;
  *
  */
 
-@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
+@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
 @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 9c5237322..2a424e15b 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
@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -110,7 +111,7 @@ import java.util.*;
  *
  */
 
-@DocumentedGATKFeature( groupName = "Variant Discovery Tools" )
+@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
 @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 555670870..98a8ac92b 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
@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub;
@@ -97,7 +98,7 @@ import java.util.*;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
+@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
 @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 eee0f33dc..235eb1d9b 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
@@ -30,6 +30,7 @@ import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -77,7 +78,7 @@ import java.util.*;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
+@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
 @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 cd25cc22d..e4831eaf2 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
@@ -25,6 +25,7 @@
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -187,7 +188,7 @@ import java.util.*;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
+@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
 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 3132db3e8..4b793a31e 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
@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broad.tribble.TribbleException;
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
 import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -67,7 +68,7 @@ import java.util.Set;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Validation Utilities" )
+@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
 @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 66a737269..a301867fc 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
@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -82,7 +83,7 @@ import java.util.*;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Validation Utilities" )
+@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
 @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 a6f8bc3aa..844c4d5fb 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
@@ -25,6 +25,7 @@
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
@@ -98,7 +99,7 @@ import java.util.*;
  * @author Mark DePristo
  * @since 2010
  */
-@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
+@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
 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 411527947..787d4d9ab 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
@@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
 import net.sf.samtools.util.CloseableIterator;
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -79,7 +80,7 @@ import java.util.*;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools" )
+@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
 @Reference(window=@Window(start=-40,stop=40))
 public class VariantsToVCF extends RodWalker<Integer, Integer> {