diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index ac4fba4b4..34c7912d9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -23,7 +23,10 @@
  */
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broadinstitute.sting.commandline.*;
+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.arguments.StandardVariantContextInputArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -49,16 +52,46 @@ import java.util.*;
 
 import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFromRods;
 
-
 /**
  * Walks along all variant ROD loci, caching a user-defined window of VariantContext sites, and then finishes phasing them when they go out of range (using upstream and downstream reads).
+ *
+ * <p>
+ * Performs physical phasing of SNP calls, based on sequencing reads.
+ * </p>
+ *
+ * <h2>Input</h2>
+ * <p>
+ * VCF file of SNP calls, BAM file of sequence reads.
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ * Phased VCF file.
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ *    java
+ *      -jar GenomeAnalysisTK.jar
+ *      -T ReadBackedPhasing
+ *      -R reference.fasta
+ *      -I reads.bam
+ *      --variant:vcf SNPs.vcf
+ *      -BTI variant
+ *      -BTIMR INTERSECTION
+ *      -o phased_SNPs.vcf
+ *      --phaseQualityThresh 20.0
+ * </pre>
+ *
+ * @author Menachem Fromer
+ * @since July 2010
  */
 @Allows(value = {DataSource.READS, DataSource.REFERENCE})
 @Requires(value = {DataSource.READS, DataSource.REFERENCE})
 @By(DataSource.READS)
 
-@ReadFilters({MappingQualityZeroReadFilter.class})
 // Filter out all reads with zero mapping quality
+@ReadFilters({MappingQualityZeroReadFilter.class})
 
 public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, PhasingStats> {
     private static final boolean DEBUG = false;
@@ -73,13 +106,13 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
     @Output(doc = "File to which variants should be written", required = true)
     protected VCFWriter writer = null;
 
-    @Argument(fullName = "cacheWindowSize", shortName = "cacheWindow", doc = "The window size (in bases) to cache variant sites and their reads; [default:20000]", required = false)
+    @Argument(fullName = "cacheWindowSize", shortName = "cacheWindow", doc = "The window size (in bases) to cache variant sites and their reads for the phasing procedure", required = false)
     protected Integer cacheWindow = 20000;
 
-    @Argument(fullName = "maxPhaseSites", shortName = "maxSites", doc = "The maximum number of successive heterozygous sites permitted to be used by the phasing algorithm; [default:10]", required = false)
+    @Argument(fullName = "maxPhaseSites", shortName = "maxSites", doc = "The maximum number of successive heterozygous sites permitted to be used by the phasing algorithm", required = false)
     protected Integer maxPhaseSites = 10; // 2^10 == 10^3 diploid haplotypes
 
-    @Argument(fullName = "phaseQualityThresh", shortName = "phaseThresh", doc = "The minimum phasing quality score required to output phasing; [default:10.0]", required = false)
+    @Argument(fullName = "phaseQualityThresh", shortName = "phaseThresh", doc = "The minimum phasing quality score required to output phasing", required = false)
     protected Double phaseQualityThresh = 10.0; // PQ = 10.0 <=> P(error) = 10^(-10/10) = 0.1, P(correct) = 0.9
 
     @Hidden
@@ -87,10 +120,10 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
     protected String variantStatsFilePrefix = null;
     private PhasingQualityStatsWriter statsWriter = null;
 
-    @Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for phasing [default: 17]", required = false)
+    @Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for phasing", required = false)
     public int MIN_BASE_QUALITY_SCORE = 17;
 
-    @Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for phasing [default: 20]", required = false)
+    @Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for phasing", required = false)
     public int MIN_MAPPING_QUALITY_SCORE = 20;
 
     @Argument(fullName = "sampleToPhase", shortName = "sampleToPhase", doc = "Only include these samples when phasing", required = false)
@@ -111,10 +144,10 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
 
     public static final String PHASING_INCONSISTENT_KEY = "PhasingInconsistent";
 
-    @Argument(fullName = "enableMergePhasedSegregatingPolymorphismsToMNP", shortName = "enableMergeToMNP", doc = "Merge consecutive phased sites into MNP records [default:false]", required = false)
+    @Argument(fullName = "enableMergePhasedSegregatingPolymorphismsToMNP", shortName = "enableMergeToMNP", doc = "Merge consecutive phased sites into MNP records", required = false)
     protected boolean enableMergePhasedSegregatingPolymorphismsToMNP = false;
 
-    @Argument(fullName = "maxGenomicDistanceForMNP", shortName = "maxDistMNP", doc = "The maximum reference-genome distance between consecutive heterozygous sites to permit merging phased VCF records into a MNP record; [default:1]", required = false)
+    @Argument(fullName = "maxGenomicDistanceForMNP", shortName = "maxDistMNP", doc = "The maximum reference-genome distance between consecutive heterozygous sites to permit merging phased VCF records into a MNP record", required = false)
     protected int maxGenomicDistanceForMNP = 1;
 
     @Hidden