diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
index 4332a6def..f56a43c0b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
@@ -110,7 +110,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
     private long countedBases = 0; // Number of bases used in the calculations, used for reporting in the output file
     private long skippedSites = 0; // Number of loci skipped because it was a dbSNP site, used for reporting in the output file
     private int numUnprocessed = 0; // Number of consecutive loci skipped because we are only processing every Nth site
-    private final String versionNumber = "2.0.4"; // Major version, minor version, and build number
+    private final String versionString = "v2.0.4"; // Major version, minor version, and build number
     private Pair<Long, Long> dbSNP_counts = new Pair<Long, Long>(0L, 0L);  // mismatch/base counts for dbSNP loci
     private Pair<Long, Long> novel_counts = new Pair<Long, Long>(0L, 0L);  // mismatch/base counts for non-dbSNP loci
     private static final double DBSNP_VS_NOVEL_MISMATCH_RATE = 2.0;        // rate at which dbSNP sites (on an individual level) mismatch relative to novel sites (determined by looking at NA12878)
@@ -130,7 +130,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
      */
     public void initialize() {
 
-        logger.info( "CovariateCounterWalker version: " + versionNumber );
+        logger.info( "CovariateCounterWalker version: " + versionString );
 
         // Get a list of all available covariates
         final List<Class<? extends Covariate>> classes = PackageUtils.getClassesImplementingInterface( Covariate.class );
@@ -312,7 +312,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
                             throw new RuntimeException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG, read.getReadName()));
                         }
                     }
-                    bases = read.getReadBases(); // BUGBUG: DinucCovariate is relying on this method returning the same byte for bases 'a' and 'A'. Is this true?
+                    bases = read.getReadBases(); // BUGBUG: DinucCovariate is relying on this method returning the same byte for bases 'a' and 'A'.
                     isNegStrand = read.getReadNegativeStrandFlag();
                     final SAMReadGroupRecord readGroup = read.getReadGroup();
                     if( readGroup == null ) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
index 57dbf902b..87d607b44 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
@@ -168,6 +168,9 @@ public class RecalDataManager {
         dataSumExpectedErrors.clear();
         dataCollapsedReadGroup.clear();
         dataCollapsedQualityScore.clear();
+        for( int iii = 0; iii < numCovariates - 2; iii++ ) {
+            dataCollapsedByCovariate.get(iii).clear();
+        }
         dataCollapsedByCovariate.clear();
         dataSumExpectedErrors = null; // Will never need this table again
         dataCollapsedReadGroup = null; // Will never need this table again
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index 9cd60c2a1..4a7cf91cf 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import net.sf.samtools.*;
-import net.sf.picard.reference.ReferenceSequenceFileFactory;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.gatk.walkers.Requires;
@@ -66,8 +65,8 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
     /////////////////////////////
     @Argument(fullName="recal_file", shortName="recalFile", doc="Input recalibration table file generated by CountCovariates", required=true)
     private String RECAL_FILE = null;
-    @Argument(fullName="output_bam", shortName="outputBam", doc="output BAM file", required=false)
-    private SAMFileWriter OUTPUT_BAM = null;
+    @Argument(fullName="output_bam", shortName="outputBam", doc="output BAM file", required=true)
+    private String OUTPUT_BAM_FILE = null;
     @Argument(fullName="preserve_qscores_less_than", shortName="pQ",
         doc="Bases with quality scores less than this threshold won't be recalibrated, default=5. In general its unsafe to change qualities scores below < 5, since base callers use these values to indicate random or bad bases", required=false)
     private int PRESERVE_QSCORES_LESS_THAN = 5;
@@ -87,8 +86,8 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
     private boolean USE_SLX_PLATFORM = false;
     @Argument(fullName="ignore_readgroup", shortName="noRG", required=false, doc="All read groups are combined together. FOR DEBUGGING PURPOSES ONLY. This option is required in order to pass integration tests.")
     private boolean IGNORE_READGROUP = false;
-    //@Argument(fullName="no_pg_tag", shortName="noPG", required=false, doc="Don't output the usual PG tag in the recalibrated bam file. FOR DEBUGGING PURPOSES ONLY. This option is required in order to pass integration tests.")
-    //private boolean NO_PG_TAG = false;
+    @Argument(fullName="no_pg_tag", shortName="noPG", required=false, doc="Don't output the usual PG tag in the recalibrated bam file header. FOR DEBUGGING PURPOSES ONLY. This option is required in order to pass integration tests.")
+    private boolean NO_PG_TAG = false;
 
 
     /////////////////////////////
@@ -101,8 +100,9 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
     private static Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
     private static Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
     private static Pattern COVARIATE_PATTERN = Pattern.compile("^@!.*");
-    private final String versionNumber = "2.0.2"; // Major version, minor version, and build number
+    private final String versionString = "v2.0.3"; // Major version, minor version, and build number
     private boolean warnUserNullReadGroup = false; // Has the walker warned the user about null read groups yet?
+    private SAMFileWriter OUTPUT_BAM = null;// The File Writer that will write out the recalibrated bam
 
     //---------------------------------------------------------------------------------------------------------------
     //
@@ -117,7 +117,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
      */
     public void initialize() {
 
-        logger.info( "TableRecalibrationWalker version: " + versionNumber );
+        logger.info( "TableRecalibrationWalker version: " + versionString );
 
         // Get a list of all available covariates
         List<Class<? extends Covariate>> classes = PackageUtils.getClassesImplementingInterface(Covariate.class);
@@ -216,17 +216,20 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
         dataManager.generateEmpiricalQualities( requestedCovariates.size(), SMOOTHING );
         logger.info( "...done!" );
 
-        // Take the header of the SAM file, tweak it by adding in the reference dictionary and specifying that the target file is unsorted.
-        //SAMFileHeader header = getToolkit().getSAMFileHeader().clone();
-        //SAMSequenceDictionary referenceDictionary =
-        //        ReferenceSequenceFileFactory.getReferenceSequenceFile(getToolkit().getArguments().referenceFile).getSequenceDictionary();
-        //header.setSequenceDictionary(referenceDictionary);
-        //header.setSortOrder(SAMFileHeader.SortOrder.unsorted);
+        // Take the header of the input SAM file and tweak it by adding in a new programRecord with the version number and list of covariates that were used
+        SAMFileHeader header = getToolkit().getSAMFileHeader().clone();
+        if( !NO_PG_TAG ) {
+            SAMProgramRecord programRecord = new SAMProgramRecord( "TableRecalibrationWalker" );
+            programRecord.setProgramVersion( versionString );
+            programRecord.setCommandLine( "Covariates used: " + requestedCovariates );
+            header.addProgramRecord( programRecord );
+        }
 
-        //if( OUTPUT_BAM != null ) {
-        //    SAMFileWriterFactory factory = new SAMFileWriterFactory();
-        //    OUTPUT_BAM = factory.makeBAMWriter(header, false, new File(OUTPUT_BAM.toString()), 5); // Bam compression = 5
-        //}
+        // Create the SAMFileWriter that we will be using to output the reads
+        if( OUTPUT_BAM_FILE != null ) {
+            SAMFileWriterFactory factory = new SAMFileWriterFactory();
+            OUTPUT_BAM = factory.makeBAMWriter( header, true, new File(OUTPUT_BAM_FILE), 5 ); // BUGBUG: Bam compression hardcoded to 5
+        }
     }
 
     /**
@@ -482,4 +485,14 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
 
         return output;
     }
+
+    /**
+     * Close the output bam file
+     * @param output The SAMFileWriter that outputs the bam file
+     */
+    public void onTraversalDone(SAMFileWriter output) {
+        if (output != null)
+            output.close();
+        super.onTraversalDone(output);
+    }
 }
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
index a0e236ac4..230179740 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -66,6 +66,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
                                 ( bam.equals( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" )
                                     ? " -L 1:10,800,000-10,810,000" : " -L 1:10,100,000-10,300,000" ) +
                                 " -outputBam %s" +
+                                " --no_pg_tag" +
                                 " -recalFile " + paramsFile,
                         1, // just one output file
                         Arrays.asList(md5));