diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
index 40e6748ed..aca176bc2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
@@ -48,6 +48,31 @@ import static java.lang.Math.log10;
 
 /**
  * Takes files produced by Beagle imputation engine and creates a vcf with modified annotations.
+ *
+ * <p>This walker is intended to be run after Beagle has successfully executed. The full calling sequence for using Beagle along with the GATK is:      </p>
+ *
+ * <p>1. Run ProduceBeagleInputWalker.  </p>
+ * <p>2. Run Beagle</p>
+ * <p>3. Uncompress output files</p>
+ * <p>4. Run BeagleOutputToVCFWalker.</p>
+ *
+ *
+ * Note that this walker requires all input files produced by Beagle.
+ *
+ *
+ * <h2>Example</h2>
+ * <pre>
+ *     java -Xmx4000m -jar dist/GenomeAnalysisTK.jar \
+ *      -R reffile.fasta -T BeagleOutputToVCF \
+ *      -B:variant,VCF input_vcf.vcf \
+ *      -B:beagleR2,BEAGLE /myrun.beagle_output.r2 \
+ *      -B:beaglePhased,BEAGLE /myrun.beagle_output.phased \
+ *      -B:beagleProbs,BEAGLE /myrun.beagle_output.gprobs \
+ *      --out output_vcf.vcf
+ *      </pre>
+
+ <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>
+
  */
 public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
 
@@ -57,22 +82,18 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
     @Input(fullName="comp", shortName = "comp", doc="Comparison VCF file", required=false)
     public RodBinding<VariantContext> comp;
 
-    @Input(fullName="beagleR2", shortName = "beagleR2", doc="VCF file", required=true)
+    @Input(fullName="beagleR2", shortName = "beagleR2", doc="Beagle-produced .r2 file containing R^2 values for all markers", required=true)
     public RodBinding<BeagleFeature> beagleR2;
 
-    @Input(fullName="beagleProbs", shortName = "beagleProbs", doc="VCF file", required=true)
+    @Input(fullName="beagleProbs", shortName = "beagleProbs", doc="Beagle-produced .probs file containing posterior genotype probabilities", required=true)
     public RodBinding<BeagleFeature> beagleProbs;
 
-    @Input(fullName="beaglePhased", shortName = "beaglePhased", doc="VCF file", required=true)
+    @Input(fullName="beaglePhased", shortName = "beaglePhased", doc="Beagle-produced .phased file containing phased genotypes", required=true)
     public RodBinding<BeagleFeature> beaglePhased;
 
-    @Output(doc="File to which variants should be written",required=true)
+    @Output(doc="VCF File to which variants should be written",required=true)
     protected VCFWriter vcfWriter = null;
 
-    @Argument(fullName="output_file", shortName="output", doc="Please use --out instead" ,required=false)
-    @Deprecated
-    protected String oldOutputArg;
-
     @Argument(fullName="dont_mark_monomorphic_sites_as_filtered", shortName="keep_monomorphic", doc="If provided, we won't filter sites that beagle tags as monomorphic.  Useful for imputing a sample's genotypes from a reference panel" ,required=false)
     public boolean DONT_FILTER_MONOMORPHIC_SITES = false;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
index c1508cf83..6ac817555 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
@@ -48,19 +48,45 @@ import java.io.PrintStream;
 import java.util.*;
 
 /**
- * Produces an input file to Beagle imputation engine, listing genotype likelihoods for each sample in input variant file
+ *  Converts the input VCF into a format accepted by the Beagle imputation/analysis program.
+ * <p>
+ *
+ * <h2>Input</h2>
+ * <p>
+ * A VCF with variants to convert to Beagle format
+ * </p>
+ *
+ * <h2>Outputs</h2>
+ * <p>
+ * A single text file which can be fed to Beagle
+ * </p>
+ * <p>
+ * Optional: A file with a list of markers
+ * </p>
+  *
+ * <h2>Examples</h2>
+ * <pre>
+ *     java -Xmx2g -jar dist/GenomeAnalysisTK.jar -L 20 \
+ *      -R reffile.fasta -T ProduceBeagleInput \
+ *      -B:variant,VCF path_to_input_vcf/inputvcf.vcf -o path_to_beagle_output/beagle_output
+ * </pre>
+ *
  */
+
 public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
 
     @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
 
-    @Input(fullName="validation", shortName = "validation", doc="Input VCF file", required=false)
+    @Hidden
+    @Input(fullName="validation", shortName = "validation", doc="Validation VCF file", required=false)
     public RodBinding<VariantContext> validation;
 
+
     @Output(doc="File to which BEAGLE input should be written",required=true)
     protected PrintStream  beagleWriter = null;
 
-    @Output(doc="File to which BEAGLE markers should be written", shortName="markers", fullName = "markers", required = false)
+    @Hidden
+     @Output(doc="File to which BEAGLE markers should be written", shortName="markers", fullName = "markers", required = false)
     protected PrintStream  markers = null;
     int markerCounter = 1;
 
@@ -73,14 +99,19 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
     @Argument(doc="VQSqual key", shortName = "vqskey", required=false)
     protected String VQSLOD_KEY = "VQSqual";
 
-    @Argument(fullName = "inserted_nocall_rate", shortName = "nc_rate", doc = "Rate (0-1) at which genotype no-calls will be randomly inserted, for testing", required = false)
+    @Hidden
+     @Argument(fullName = "inserted_nocall_rate", shortName = "nc_rate", doc = "Rate (0-1) at which genotype no-calls will be randomly inserted, for testing", required = false)
     public double insertedNoCallRate  = 0;
-    @Argument(fullName = "validation_genotype_ptrue", shortName = "valp", doc = "Flat probability to assign to validation genotypes. Will override GL field.", required = false)
+    @Hidden
+     @Argument(fullName = "validation_genotype_ptrue", shortName = "valp", doc = "Flat probability to assign to validation genotypes. Will override GL field.", required = false)
     public double validationPrior = -1.0;
-    @Argument(fullName = "validation_bootstrap", shortName = "bs", doc = "Proportion of records to be used in bootstrap set", required = false)
+    @Hidden
+     @Argument(fullName = "validation_bootstrap", shortName = "bs", doc = "Proportion of records to be used in bootstrap set", required = false)
     public double bootstrap = 0.0;
-    @Argument(fullName = "bootstrap_vcf",shortName = "bvcf", doc = "Output a VCF with the records used for bootstrapping filtered out", required = false)
+    @Hidden
+     @Argument(fullName = "bootstrap_vcf",shortName = "bvcf", doc = "Output a VCF with the records used for bootstrapping filtered out", required = false)
     VCFWriter bootstrapVCFOutput = null;
+
     @Argument(fullName = "checkIsMaleOnChrX", shortName = "checkIsMaleOnChrX", doc = "Set to true when Beagle-ing chrX and want to ensure male samples don't have heterozygous calls.", required = false)
     public boolean CHECK_IS_MALE_ON_CHR_X = false;