diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.gatkreport.R b/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.gatkreport.R
index 46bbf7eda..876cf5cbc 100644
--- a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.gatkreport.R
+++ b/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.gatkreport.R
@@ -4,11 +4,9 @@
     colnames(d) = tableHeader;
 
     for (i in 1:ncol(d)) {
-        v = suppressWarnings(as.numeric(d[,i]));
-
-        if (length(na.omit(as.numeric(v))) == length(d[,i])) {
-            d[,i] = v;
-        }
+        # use the general type.convert infrastructure of read.table to convert column data to R types 
+        v = type.convert(d[,i])
+        d[,i] = v;
     }
 
     usedNames = ls(envir=tableEnv, pattern=tableName);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
index 3f555f780..00968943d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
@@ -43,15 +43,15 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements Standar
         final ArrayList<Double> altQuals = new ArrayList<Double>();
 
         if ( vc.isSNP() ) {
+            final List<Byte> altAlleles = new ArrayList<Byte>();
+            for ( final Allele a : vc.getAlternateAlleles() )
+                altAlleles.add(a.getBases()[0]);
+
             for ( final Genotype genotype : genotypes.iterateInSampleNameOrder() ) {
                 final AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
                 if ( context == null )
                     continue;
 
-                final List<Byte> altAlleles = new ArrayList<Byte>();
-                for ( final Allele a : vc.getAlternateAlleles() )
-                    altAlleles.add(a.getBases()[0]);
-                
                 fillQualsFromPileup(ref.getBase(), altAlleles, context.getBasePileup(), refQuals, altQuals);
             }
         } else if ( vc.isIndel() || vc.isMixed() ) {
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 c192d04e7..d7a48d321 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
@@ -36,13 +36,14 @@ import org.broadinstitute.sting.utils.Median;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.io.PrintStream;
+import java.text.DateFormat;
 import java.util.HashMap;
 import java.util.Map;
 
 /**
- * Emits a GATKReport containing read group, sample, library, platform, center, paired end status,
- * simple read type name (e.g. 2x76) median insert size and median read length for each read group
- * in every provided BAM file
+ * Emits a GATKReport containing read group, sample, library, platform, center, sequencing data,
+ * paired end status, simple read type name (e.g. 2x76) median insert size and median read length
+ * for each read group in every provided BAM file
  *
  * Note that this walker stops when all read groups have been observed at least a few thousand times so that
  * the median statistics are well determined.  It is safe to run it WG and it'll finish in an appropriate
@@ -61,23 +62,23 @@ import java.util.Map;
  *
  *      <pre>
  *      ##:GATKReport.v0.2 ReadGroupProperties : Table of read group properties
- *      readgroup  sample   library       platform  center  has.any.reads  is.paired.end  n.reads.analyzed  simple.read.type  median.read.length  median.insert.size
- *      20FUK.1    NA12878  Solexa-18483  illumina  BI      true           true                      10100  2x101                            101                 387
- *      20FUK.2    NA12878  Solexa-18484  illumina  BI      true           true                      10115  2x101                            101                 415
- *      20FUK.3    NA12878  Solexa-18483  illumina  BI      true           true                      10090  2x101                            101                 388
- *      20FUK.4    NA12878  Solexa-18484  illumina  BI      true           true                      10081  2x101                            101                 415
- *      20FUK.5    NA12878  Solexa-18483  illumina  BI      true           true                      10078  2x101                            101                 387
- *      20FUK.6    NA12878  Solexa-18484  illumina  BI      true           true                      10072  2x101                            101                 415
- *      20FUK.7    NA12878  Solexa-18483  illumina  BI      true           true                      10086  2x101                            101                 388
- *      20FUK.8    NA12878  Solexa-18484  illumina  BI      true           true                      10097  2x101                            101                 415
- *      20GAV.1    NA12878  Solexa-18483  illumina  BI      true           true                      10135  2x101                            101                 388
- *      20GAV.2    NA12878  Solexa-18484  illumina  BI      true           true                      10172  2x101                            101                 415
- *      20GAV.3    NA12878  Solexa-18483  illumina  BI      true           true                      10141  2x101                            101                 388
- *      20GAV.4    NA12878  Solexa-18484  illumina  BI      true           true                      10251  2x101                            101                 416
- *      20GAV.5    NA12878  Solexa-18483  illumina  BI      true           true                      10145  2x101                            101                 388
- *      20GAV.6    NA12878  Solexa-18484  illumina  BI      true           true                      10184  2x101                            101                 415
- *      20GAV.7    NA12878  Solexa-18483  illumina  BI      true           true                      10174  2x101                            101                 387
- *      20GAV.8    NA12878  Solexa-18484  illumina  BI      true           true                      10141  2x101                            101                 414
+ *      readgroup  sample   library       platform  center  date     has.any.reads  is.paired.end  n.reads.analyzed  simple.read.type  median.read.length  median.insert.size
+ *      20FUK.1    NA12878  Solexa-18483  illumina  BI      2/2/10   true           true                        498  2x101                            101                 386
+ *      20FUK.2    NA12878  Solexa-18484  illumina  BI      2/2/10   true           true                        476  2x101                            101                 417
+ *      20FUK.3    NA12878  Solexa-18483  illumina  BI      2/2/10   true           true                        407  2x101                            101                 387
+ *      20FUK.4    NA12878  Solexa-18484  illumina  BI      2/2/10   true           true                        389  2x101                            101                 415
+ *      20FUK.5    NA12878  Solexa-18483  illumina  BI      2/2/10   true           true                        433  2x101                            101                 386
+ *      20FUK.6    NA12878  Solexa-18484  illumina  BI      2/2/10   true           true                        480  2x101                            101                 418
+ *      20FUK.7    NA12878  Solexa-18483  illumina  BI      2/2/10   true           true                        450  2x101                            101                 386
+ *      20FUK.8    NA12878  Solexa-18484  illumina  BI      2/2/10   true           true                        438  2x101                            101                 418
+ *      20GAV.1    NA12878  Solexa-18483  illumina  BI      1/26/10  true           true                        490  2x101                            101                 391
+ *      20GAV.2    NA12878  Solexa-18484  illumina  BI      1/26/10  true           true                        485  2x101                            101                 417
+ *      20GAV.3    NA12878  Solexa-18483  illumina  BI      1/26/10  true           true                        460  2x101                            101                 392
+ *      20GAV.4    NA12878  Solexa-18484  illumina  BI      1/26/10  true           true                        434  2x101                            101                 415
+ *      20GAV.5    NA12878  Solexa-18483  illumina  BI      1/26/10  true           true                        479  2x101                            101                 389
+ *      20GAV.6    NA12878  Solexa-18484  illumina  BI      1/26/10  true           true                        461  2x101                            101                 416
+ *      20GAV.7    NA12878  Solexa-18483  illumina  BI      1/26/10  true           true                        509  2x101                            101                 386
+ *      20GAV.8    NA12878  Solexa-18484  illumina  BI      1/26/10  true           true                        476  2x101                            101                 410                           101                 414
  *      </pre>
  *  </p>
  *
@@ -172,6 +173,7 @@ public class ReadGroupProperties extends ReadWalker<Integer, Integer> {
         final GATKReport report = new GATKReport();
         report.addTable(TABLE_NAME, "Table of read group properties");
         GATKReportTable table = report.getTable(TABLE_NAME);
+        DateFormat dateFormatter = DateFormat.getDateInstance(DateFormat.SHORT);
 
         table.addPrimaryKey("readgroup");
         //* Emits a GATKReport containing read group, sample, library, platform, center, median insert size and
@@ -180,6 +182,7 @@ public class ReadGroupProperties extends ReadWalker<Integer, Integer> {
         table.addColumn("library", "NA");
         table.addColumn("platform", "NA");
         table.addColumn("center", "NA");
+        table.addColumn("date", "NA");
         table.addColumn("has.any.reads", "false");
         table.addColumn("is.paired.end", "false");
         table.addColumn("n.reads.analyzed", "NA");
@@ -196,18 +199,28 @@ public class ReadGroupProperties extends ReadWalker<Integer, Integer> {
             final boolean hasAnyReads = info.nReadsSeen > 0;
             final int readLength = info.readLength.getMedian(0);
 
-            table.set(rgID, "sample", rg.getSample());
-            table.set(rgID, "library", rg.getLibrary());
-            table.set(rgID, "platform", rg.getPlatform());
-            table.set(rgID, "center", rg.getSequencingCenter());
-            table.set(rgID, "has.any.reads", hasAnyReads);
-            table.set(rgID, "is.paired.end", isPaired);
-            table.set(rgID, "n.reads.analyzed", info.nReadsSeen);
-            table.set(rgID, "simple.read.type", hasAnyReads ? String.format("%dx%d", isPaired ? 2 : 1, readLength) : "NA");
-            table.set(rgID, "median.read.length", hasAnyReads ? readLength : "NA" );
-            table.set(rgID, "median.insert.size", hasAnyReads && isPaired ? info.insertSize.getMedian(0) : "NA" );
+            setTableValue(table, rgID, "sample", rg.getSample());
+            setTableValue(table, rgID, "library", rg.getLibrary());
+            setTableValue(table, rgID, "platform", rg.getPlatform());
+            setTableValue(table, rgID, "center", rg.getSequencingCenter());
+            try {
+                setTableValue(table, rgID, "date", rg.getRunDate() != null ? dateFormatter.format(rg.getRunDate()) : "NA");
+            } catch ( NullPointerException e ) {
+                // TODO: remove me when bug in Picard is fixed that causes NPE when date isn't present
+                setTableValue(table, rgID, "date", "NA");
+            }
+            setTableValue(table, rgID, "has.any.reads", hasAnyReads);
+            setTableValue(table, rgID, "is.paired.end", isPaired);
+            setTableValue(table, rgID, "n.reads.analyzed", info.nReadsSeen);
+            setTableValue(table, rgID, "simple.read.type", hasAnyReads ? String.format("%dx%d", isPaired ? 2 : 1, readLength) : "NA");
+            setTableValue(table, rgID, "median.read.length", hasAnyReads ? readLength : "NA" );
+            setTableValue(table, rgID, "median.insert.size", hasAnyReads && isPaired ? info.insertSize.getMedian(0) : "NA" );
         }
 
         report.print(out);
     }
+
+    private final void setTableValue(GATKReportTable table, final String rgID, final String key, final Object value) {
+        table.set(rgID, key, value == null ? "NA" : value);
+    }
 }
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 b27bef265..e812fb53a 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
@@ -110,6 +110,13 @@ public class ValidationAmplicons extends RodWalker<Integer,Integer> {
     @Argument(doc="Lower case SNPs rather than replacing with 'N'",fullName="lowerCaseSNPs",required=false)
     boolean lowerCaseSNPs = false;
 
+    /**
+     * If onlyOutputValidAmplicons is true, the output fasta file will contain only valid sequences.
+     * Useful for producing delivery-ready files.
+     */
+    @Argument(doc="Only output valid sequences.",fullName="onlyOutputValidAmplicons",required=false)
+    boolean onlyOutputValidAmplicons = false;
+
     /**
      * BWA single-end alignment is used as a primer specificity proxy. Low-complexity regions (that don't align back to themselves as a best hit) are lowercased.
      * This changes the size of the k-mer used for alignment.
@@ -486,14 +493,16 @@ public class ValidationAmplicons extends RodWalker<Integer,Integer> {
             valid = "Valid";
         }
 
-        String seqIdentity = sequence.toString().replace('n', 'N').replace('i', 'I').replace('d', 'D');
 
-        if (!sequenomOutput)
-            out.printf(">%s %s %s%n%s%n", allelePos != null ? allelePos.toString() : "multiple", valid, probeName, seqIdentity);
-        else {
-            seqIdentity = seqIdentity.replace("*",""); // identifier < 20 letters long, no * in ref allele, one line per record
-            probeName = probeName.replace("amplicon_","a");
-            out.printf("%s_%s %s%n", allelePos != null ? allelePos.toString() : "multiple", probeName, seqIdentity);
+        if (!onlyOutputValidAmplicons || !sequenceInvalid) {
+            String seqIdentity = sequence.toString().replace('n', 'N').replace('i', 'I').replace('d', 'D');
+            if (!sequenomOutput)
+                out.printf(">%s %s %s%n%s%n", allelePos != null ? allelePos.toString() : "multiple", valid, probeName, seqIdentity);
+            else {
+                seqIdentity = seqIdentity.replace("*",""); // identifier < 20 letters long, no * in ref allele, one line per record
+                probeName = probeName.replace("amplicon_","a");
+                out.printf("%s_%s %s%n", allelePos != null ? allelePos.toString() : "multiple", probeName, seqIdentity);
+            }
         }
     }
 }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java
index 04c30a8fe..1a4c8db30 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java
@@ -38,7 +38,7 @@ public class ReadGroupPropertiesIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T ReadGroupProperties -R " + b37KGReference + " -I " + b37GoodBAM + " -L 20:10,000,000-11,000,000 -o %s",
                 1,
-                Arrays.asList("8e4d09665c0b65c971bd5dead24f95fe"));
+                Arrays.asList("6b8cce223af28cbadcfe87a3b841fc56"));
         executeTest("ReadGroupProperties:", spec);
     }
 }
\ No newline at end of file