diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/BaseLikelihoodsFileReader.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/BaseLikelihoodsFileReader.java
index b6647c3af..06acd5789 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/BaseLikelihoodsFileReader.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/BaseLikelihoodsFileReader.java
@@ -1,13 +1,9 @@
-/*
- * Reads the .baselikelihoods file for various walkers in the HLA caller suite
- */
- 
 package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
 
 import java.io.*;
 import java.util.ArrayList;
 /**
- *
+ * Reads the .baselikelihoods file for various walkers in the HLA caller suite
  * @author shermanjia
  */
 public class BaseLikelihoodsFileReader {
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateAlleleLikelihoodsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateAlleleLikelihoodsWalker.java
index c5c68e6c6..29a344532 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateAlleleLikelihoodsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateAlleleLikelihoodsWalker.java
@@ -1,9 +1,5 @@
-/*
- * Calculates likelihood of observing the data given pairs of HLA alleles. NOTE: run CalculateBaseLikelihoods first! Usage: java -jar GenomeAnalysisTK.jar -T CalculateAlleleLikelihoods -I /humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA.nuc.imputed.4digit.bam -R /broad/1KG/reference/human_b36_both.fasta -L /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval -bl INPUT.baselikelihoods -eth\
-nicity Caucasian | grep -v "INFO"  | grep -v "DONE!" > OUTPUT.allelelikelihoods
- */
-
 package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
+
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
@@ -13,7 +9,8 @@ import java.util.Hashtable;
 
 
 /**
- *
+ * Calculates likelihood of observing the data given pairs of HLA alleles. NOTE: run CalculateBaseLikelihoods first! Usage: java -jar GenomeAnalysisTK.jar -T CalculateAlleleLikelihoods -I /humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA.nuc.imputed.4digit.bam -R /broad/1KG/reference/human_b36_both.fasta -L /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval -bl INPUT.baselikelihoods -eth\
+nicity Caucasian | grep -v "INFO"  | grep -v "DONE!" > OUTPUT.allelelikelihoods
  * @author shermanjia
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java
index 02d6cf0aa..48439fe39 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java
@@ -1,8 +1,5 @@
-/*
- * Calculates the probability of observing data for each genotype at every position. NOTE: run FindClosestAllele first to create .filter file. Usage: java -jar GenomeAnalysisTK.jar -T CalculateBaseLikelihoods -I INPUT.bam -R /broad/1KG/reference/human_b36_both.fasta -L /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval [-filter INPUT.filter -minAllowedMismatches 7] | grep -v "INFO" | grep -v "MISALIGNED" > OUTPUT.baselikelihoods
- */
-
 package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
+
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -18,7 +15,7 @@ import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
 /**
- *
+ * Calculates the probability of observing data for each genotype at every position. NOTE: run FindClosestAllele first to create .filter file. Usage: java -jar GenomeAnalysisTK.jar -T CalculateBaseLikelihoods -I INPUT.bam -R /broad/1KG/reference/human_b36_both.fasta -L /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval [-filter INPUT.filter -minAllowedMismatches 7] | grep -v "INFO" | grep -v "MISALIGNED" > OUTPUT.baselikelihoods
  * @author shermanjia
  */
 public class CalculateBaseLikelihoodsWalker extends LocusWalker<Integer, Pair<Long, Long>>{
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculatePhaseLikelihoodsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculatePhaseLikelihoodsWalker.java
index af0bfd427..31cef5e47 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculatePhaseLikelihoodsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculatePhaseLikelihoodsWalker.java
@@ -1,9 +1,5 @@
-/*
- * Calculates the likelihood of observing data given phase info from pairs of HLA alleles. Note: Run FindClosestAlleleWalker first! Usage: java -jar $GATK -T CalculatePhaseLikelihoods -I INPUT.bam -R /broad/1KG/reference/human_b36_both.fasta -L /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval -phaseInterval /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval -bl IMPUT.baselikelihoods [-filter $ID.filter -minAllowe\
-dMismatches 7] -ethnicity Caucasian | grep -v "INFO"  | grep -v "DEBUG" | grep -v "DONE!" > OUTPUT.phaselikelihoods
- */
-
 package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
+
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.GATKArgumentCollection;
@@ -13,7 +9,8 @@ import java.util.ArrayList;
 import java.util.Hashtable;
 
 /**
- *
+ * Calculates the likelihood of observing data given phase info from pairs of HLA alleles. Note: Run FindClosestAlleleWalker first! Usage: java -jar $GATK -T CalculatePhaseLikelihoods -I INPUT.bam -R /broad/1KG/reference/human_b36_both.fasta -L /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval -phaseInterval /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval -bl IMPUT.baselikelihoods [-filter $ID.filter -minAllowe\
+dMismatches 7] -ethnicity Caucasian | grep -v "INFO"  | grep -v "DEBUG" | grep -v "DONE!" > OUTPUT.phaselikelihoods
  * @author shermanjia
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java
index 92b0bff39..f059d8fb5 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java
@@ -1,9 +1,5 @@
-/**
- * Creates a ped file of SNPs and amino acids coded as SNPs given an input ped file with 4-digit HLA alleles. Usage: java -jar GenomeAnalysisTK.jar -T CreatePedFile --allelesFile INPUT.ped -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-sc\
-r1/GSA/sjia/454_HLA/HLA/HLA.combined.4digitUnique.bam > OUTPUT.log
- */
-
 package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
+
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
@@ -12,7 +8,8 @@ import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.Enumeration;
 /**
- *
+ * Creates a ped file of SNPs and amino acids coded as SNPs given an input ped file with 4-digit HLA alleles. Usage: java -jar GenomeAnalysisTK.jar -T CreatePedFile --allelesFile INPUT.ped -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-sc\
+r1/GSA/sjia/454_HLA/HLA/HLA.combined.4digitUnique.bam > OUTPUT.log
  * @author shermanjia
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestAlleleWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestAlleleWalker.java
index 892945762..a2978bf80 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestAlleleWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestAlleleWalker.java
@@ -1,7 +1,3 @@
-/**
- * Finds the most similar HLA allele for each read. Usage: java -jar GenomeAnalysisTK.jar -T FindClosestAllele -I INPUT.bam -R /broad/1KG/reference/human_b36_both.fasta -L INPUT.interval -findFirst | grep -v INFO | sort -k1 > OUTPUT
- */
-
 package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
 
 import net.sf.samtools.SAMRecord;
@@ -11,7 +7,7 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
 import java.util.ArrayList;
 import java.util.Hashtable;
 /**
- *
+ * Finds the most similar HLA allele for each read. Usage: java -jar GenomeAnalysisTK.jar -T FindClosestAllele -I INPUT.bam -R /broad/1KG/reference/human_b36_both.fasta -L INPUT.interval -findFirst | grep -v INFO | sort -k1 > OUTPUT
  * @author shermanjia
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FrequencyFileReader.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FrequencyFileReader.java
index 986c4cb26..7f18c94ed 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FrequencyFileReader.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FrequencyFileReader.java
@@ -1,13 +1,9 @@
-/**
- * File reader used by other Walkers to read HLA allele frequencies.
- */
-
 package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
 
 import java.io.*;
 import java.util.Hashtable;
 /**
- *
+ * File reader used by other Walkers to read HLA allele frequencies.
  * @author shermanjia
  */
 public class FrequencyFileReader {