diff --git a/java/src/org/broad/tribble/vcf/VCFCodec.java b/java/src/org/broad/tribble/vcf/VCFCodec.java
index cb400fff3..0f6a378c0 100644
--- a/java/src/org/broad/tribble/vcf/VCFCodec.java
+++ b/java/src/org/broad/tribble/vcf/VCFCodec.java
@@ -72,6 +72,8 @@ public class VCFCodec implements FeatureCodec {
         try {
             while ((line = reader.readLine()) != null) {
                 if (line.startsWith("##")) {
+                    if ( line.startsWith("##fileformat") && ! line.startsWith("##fileformat=VCFv3" ) )
+                        throw new CodecLineParsingException("VCF codec can only parse VCF3 formated files.  Your version line is " + line + ".  If you want to parse VCF4, use VCF4 use VCF as the rod type");
                     headerStrings.add(line);
                 }
                 else if (line.startsWith("#")) {
diff --git a/java/src/org/broad/tribble/vcf/VCFHeaderLine.java b/java/src/org/broad/tribble/vcf/VCFHeaderLine.java
index fda574a3e..f3dadccf5 100644
--- a/java/src/org/broad/tribble/vcf/VCFHeaderLine.java
+++ b/java/src/org/broad/tribble/vcf/VCFHeaderLine.java
@@ -42,6 +42,7 @@ public class VCFHeaderLine implements Comparable {
     private String stringRep = null;
     private String mKey = null;
     private String mValue = null;
+
     protected VCFHeaderVersion mVersion = null;
 
     /**
@@ -135,6 +136,10 @@ public class VCFHeaderLine implements Comparable {
         this.mVersion = version;
     }
 
+    public VCFHeaderVersion getVersion() {
+        return mVersion;
+    }
+
     /**
      * create a string of a mapping pair for the target VCF version
      * @param keyValues a mapping of the key->value pairs to output
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java
index 90afdd594..014a3b5c5 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java
@@ -80,6 +80,8 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
             while ((line = reader.readLine()) != null) {
                 lineNo++;
                 if (line.startsWith("##")) {
+                    if ( line.startsWith("##fileformat") && ! line.startsWith("##fileformat=VCFv4" ) )
+                        throw new CodecLineParsingException("VCF4 codec can only parse VCF4 formated files.  Your version line is " + line + ".  If you want VCF3 parsing, use VCF as the rod type.");
                     headerStrings.add(line);
                 }
                 else if (line.startsWith("#")) {
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 4232bdf92..54c1a8995 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
@@ -70,7 +70,7 @@ import java.util.Map;
 @WalkerName( "CountCovariates" )
 @ReadFilters( {ZeroMappingQualityReadFilter.class} ) // Filter out all reads with zero mapping quality
 @Requires( {DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES} ) // This walker requires both -I input.bam and -R reference.fasta
-public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
+public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> implements TreeReducible<PrintStream> {
 
     /////////////////////////////
     // Constants
@@ -87,6 +87,9 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
     /////////////////////////////
     // Command Line Arguments
     /////////////////////////////
+    @Argument(fullName="recal_file", shortName="recalFile", required=true, doc="Filename for the outputted covariates table recalibration file")
+    public PrintStream RECAL_FILE;
+
     @Argument(fullName="list", shortName="ls", doc="List the available covariates and exit", required=false)
     private boolean LIST_ONLY = false;
     @Argument(fullName="covariate", shortName="cov", doc="Covariates to be used in the recalibration. Each covariate is given as a separate cov parameter. ReadGroup and ReportedQuality are required covariates and are already added for you.", required=false)
@@ -230,6 +233,12 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
             logger.info( "\t" + cov.getClass().getSimpleName() );
             cov.initialize( RAC ); // Initialize any covariate member variables using the shared argument collection
         }
+
+//        try {
+//            stream = new PrintStream( RAC.RECAL_FILE );
+//        } catch ( FileNotFoundException e ) {
+//            throw new RuntimeException( "Couldn't open output file: ", e );
+//        }
     }
 
 
@@ -263,15 +272,10 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
         if( !isSNP && ( ++numUnprocessed >= PROCESS_EVERY_NTH_LOCUS ) ) {
             numUnprocessed = 0; // Reset the counter because we are processing this very locus
 
-            GATKSAMRecord gatkRead;
-            int offset;
-            byte refBase;
-            byte[] bases;
-
             // For each read at this locus
             for( PileupElement p : context.getBasePileup() ) {
-                gatkRead = (GATKSAMRecord) p.getRead();
-                offset = p.getOffset();
+                GATKSAMRecord gatkRead = (GATKSAMRecord) p.getRead();
+                int offset = p.getOffset();
 
                 if( gatkRead.containsTemporaryAttribute( SKIP_RECORD_ATTRIBUTE  ) ) {
                     continue;
@@ -297,8 +301,8 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
                 // Skip this position if base quality is zero
                 if( gatkRead.getBaseQualities()[offset] > 0 ) {
 
-                    bases = gatkRead.getReadBases();
-                    refBase = ref.getBase();
+                    byte[] bases = gatkRead.getReadBases();
+                    byte refBase = ref.getBase();
 
                     // Skip if this base is an 'N' or etc.
                     if( BaseUtils.isRegularBase( bases[offset] ) ) {
@@ -390,8 +394,6 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
      * @param refBase The reference base at this locus
      */
     private void updateDataFromRead(final GATKSAMRecord gatkRead, final int offset, final byte refBase) {
-
-
         final Object[][] covars = (Comparable[][]) gatkRead.getTemporaryAttribute(COVARS_ATTRIBUTE);
         final Object[] key = covars[offset];
 
@@ -426,11 +428,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
      * @return returns A PrintStream created from the -recalFile filename argument specified to the walker
      */
     public PrintStream reduceInit() {
-        try {
-            return new PrintStream( RAC.RECAL_FILE );
-        } catch ( FileNotFoundException e ) {
-            throw new RuntimeException( "Couldn't open output file: ", e );
-        }
+        return RECAL_FILE;
     }
 
     /**
@@ -440,7 +438,11 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
      * @return returns The PrintStream used to output the CSV data
      */
     public PrintStream reduce( Integer value, PrintStream recalTableStream ) {
-        return recalTableStream; // Nothing to do here
+        return recalTableStream; // Nothing to do here, just return our open stream
+    }
+
+    public PrintStream treeReduce( PrintStream recalTableStream1, PrintStream recalTableStream2 ) {
+        return recalTableStream1; // Nothing to do here, just return our open stream
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatumOptimized.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatumOptimized.java
index b3bb58f61..c4ad3869a 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatumOptimized.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatumOptimized.java
@@ -71,22 +71,22 @@ public class RecalDatumOptimized {
     //
     //---------------------------------------------------------------------------------------------------------------
 
-    public final void increment( final long incObservations, final long incMismatches ) {
+    public synchronized final void increment( final long incObservations, final long incMismatches ) {
         numObservations += incObservations;
         numMismatches += incMismatches;
     }
 
-    public final void increment( final RecalDatumOptimized other ) {
+    public synchronized final void increment( final RecalDatumOptimized other ) {
         increment( other.numObservations, other.numMismatches );
     }
 
-    public final void increment( final List<RecalDatumOptimized> data ) {
+    public synchronized final void increment( final List<RecalDatumOptimized> data ) {
         for ( RecalDatumOptimized other : data ) {
             this.increment( other );
         }
     }
 
-    public final void increment( final char curBase, final char refBase ) {
+    public synchronized final void increment( final char curBase, final char refBase ) {
         increment( 1, BaseUtils.simpleBaseToBaseIndex(curBase) == BaseUtils.simpleBaseToBaseIndex(refBase) ? 0 : 1 ); // increment takes num observations, then num mismatches
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
index da7cf996c..62d8543a6 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
@@ -41,8 +41,6 @@ public class RecalibrationArgumentCollection {
     //////////////////////////////////
     // Shared Command Line Arguments
     //////////////////////////////////
-    @Argument(fullName="recal_file", shortName="recalFile", required=false, doc="Filename for the outputted covariates table recalibration file")
-    public String RECAL_FILE = "output.recal_data.csv";
     @Argument(fullName="default_read_group", shortName="dRG", required=false, doc="If a read has no read group then default to the provided String.")
     public String DEFAULT_READ_GROUP = null;
     @Argument(fullName="default_platform", shortName="dP", required=false, doc="If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.")
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 7d876ddff..4a8c85415 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -87,6 +87,9 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
     /////////////////////////////
     @ArgumentCollection private RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
 
+    @Argument(fullName="recal_file", shortName="recalFile", required=false, doc="Filename for the outputted covariates table recalibration file")
+    public String RECAL_FILE = "output.recal_data.csv";
+
     /////////////////////////////
     // Command Line Arguments
     /////////////////////////////
@@ -168,7 +171,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
 
         boolean sawEOF = false;
         try {
-            for ( String line : new XReadLines(new File( RAC.RECAL_FILE )) ) {
+            for ( String line : new XReadLines(new File( RECAL_FILE )) ) {
                 lineNumber++;
                 if ( EOF_MARKER.equals(line) ) {
                     sawEOF = true;
@@ -178,7 +181,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
                 // Read in the covariates that were used from the input file
                 else if( COVARIATE_PATTERN.matcher(line).matches() ) { // The line string is either specifying a covariate or is giving csv data
                     if( foundAllCovariates ) {
-                        throw new StingException( "Malformed input recalibration file. Found covariate names intermingled with data in file: " + RAC.RECAL_FILE );
+                        throw new StingException( "Malformed input recalibration file. Found covariate names intermingled with data in file: " + RECAL_FILE );
                     } else { // Found the covariate list in input file, loop through all of them and instantiate them
                         String[] vals = line.split(",");
                         for( int iii = 0; iii < vals.length - 3; iii++ ) { // There are n-3 covariates. The last three items are nObservations, nMismatch, and Qempirical
@@ -210,7 +213,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
 
                         // At this point all the covariates should have been found and initialized
                         if( requestedCovariates.size() < 2 ) {
-                            throw new StingException( "Malformed input recalibration csv file. Covariate names can't be found in file: " + RAC.RECAL_FILE );
+                            throw new StingException( "Malformed input recalibration csv file. Covariate names can't be found in file: " + RECAL_FILE );
                         }
 
                         final boolean createCollapsedTables = true;
@@ -228,7 +231,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
             }
 
         } catch ( FileNotFoundException e ) {
-            throw new StingException("Can not find input file: " + RAC.RECAL_FILE);
+            throw new StingException("Can not find input file: " + RECAL_FILE);
         } catch ( NumberFormatException e ) {
             throw new StingException("Error parsing recalibration data at line " + lineNumber + ". Perhaps your table was generated by an older version of CovariateCounterWalker.");
         }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
index b5b5d5505..5d0dbace6 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
@@ -431,6 +431,7 @@ class SampleStats implements TableType {
 class SampleSummaryStats implements TableType {
     private final static String ALL_SAMPLES_KEY = "allSamples";
     private final static String[] COLUMN_KEYS = new String[]{
+            "percent_comp_ref_called_var",
             "percent_comp_het_called_het",
             "percent_comp_het_called_var",
             "percent_comp_hom_called_hom",
@@ -532,45 +533,50 @@ class SampleSummaryStats implements TableType {
 
             long numer, denom;
 
-            // Summary 0: % het called as het
-            numer = stats[Genotype.Type.HET.ordinal()][Genotype.Type.HET.ordinal()];
-            denom = sumStatsAllPairs(stats, EnumSet.of(Genotype.Type.HET), allGenotypes);
+            // Summary 0: % ref called as var
+            numer = sumStatsAllPairs(stats, EnumSet.of(Genotype.Type.HOM_REF), allVariantGenotypes);
+            denom = sumStatsAllPairs(stats, EnumSet.of(Genotype.Type.HOM_REF), allGenotypes);
             updateSummaries(0, summary,  numer, denom);
 
-            // Summary 1: % het called as var
-            numer = sumStatsAllPairs(stats, EnumSet.of(Genotype.Type.HET), allVariantGenotypes);
+            // Summary 1: % het called as het
+            numer = stats[Genotype.Type.HET.ordinal()][Genotype.Type.HET.ordinal()];
             denom = sumStatsAllPairs(stats, EnumSet.of(Genotype.Type.HET), allGenotypes);
             updateSummaries(1, summary,  numer, denom);
 
-            // Summary 2: % homVar called as homVar
-            numer = stats[Genotype.Type.HOM_VAR.ordinal()][Genotype.Type.HOM_VAR.ordinal()];
-            denom = sumStatsAllPairs(stats, EnumSet.of(Genotype.Type.HOM_VAR), allGenotypes);
+            // Summary 2: % het called as var
+            numer = sumStatsAllPairs(stats, EnumSet.of(Genotype.Type.HET), allVariantGenotypes);
+            denom = sumStatsAllPairs(stats, EnumSet.of(Genotype.Type.HET), allGenotypes);
             updateSummaries(2, summary,  numer, denom);
 
-            // Summary 3: % homVars called as var
-            numer = sumStatsAllPairs(stats, EnumSet.of(Genotype.Type.HOM_VAR), allVariantGenotypes);
+            // Summary 3: % homVar called as homVar
+            numer = stats[Genotype.Type.HOM_VAR.ordinal()][Genotype.Type.HOM_VAR.ordinal()];
             denom = sumStatsAllPairs(stats, EnumSet.of(Genotype.Type.HOM_VAR), allGenotypes);
             updateSummaries(3, summary,  numer, denom);
 
-            // Summary 4: % non-ref called as non-ref
+            // Summary 4: % homVars called as var
+            numer = sumStatsAllPairs(stats, EnumSet.of(Genotype.Type.HOM_VAR), allVariantGenotypes);
+            denom = sumStatsAllPairs(stats, EnumSet.of(Genotype.Type.HOM_VAR), allGenotypes);
+            updateSummaries(4, summary,  numer, denom);
+
+            // Summary 5: % non-ref called as non-ref
             // MAD: this is known as the non-reference sensitivity (# non-ref according to comp found in eval / # non-ref in comp)
             numer = sumStatsAllPairs(stats, allVariantGenotypes, allVariantGenotypes);
             denom = sumStatsAllPairs(stats, allVariantGenotypes, allGenotypes);
-            updateSummaries(4, summary,  numer, denom);
+            updateSummaries(5, summary,  numer, denom);
 
-            // Summary 5: overall genotype concordance of sites called in eval track
+            // Summary 6: overall genotype concordance of sites called in eval track
             // MAD: this is the tradition genotype concordance
             numer = sumStatsDiag(stats, allCalledGenotypes);
             denom = sumStatsAllPairs(stats, allCalledGenotypes, allCalledGenotypes);
-            updateSummaries(5, summary,  numer, denom);
+            updateSummaries(6, summary,  numer, denom);
 
-            // Summary 6: overall genotype concordance of sites called non-ref in eval track
+            // Summary 7: overall genotype concordance of sites called non-ref in eval track
             long homrefConcords = stats[Genotype.Type.HOM_REF.ordinal()][Genotype.Type.HOM_REF.ordinal()];
             long diag = sumStatsDiag(stats, allVariantGenotypes);
             long allNoHomRef = sumStatsAllPairs(stats, allCalledGenotypes, allCalledGenotypes) - homrefConcords;
             numer = allNoHomRef - diag;
             denom = allNoHomRef;
-            updateSummaries(6, summary,  numer, denom);
+            updateSummaries(7, summary,  numer, denom);
         }
 
         // update the final summary stats
diff --git a/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java b/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java
index 9b4bc1e63..e383a6f7c 100755
--- a/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java
+++ b/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java
@@ -52,7 +52,7 @@ public class NestedHashMap{
         return null;
     }
 
-    public void put( final Object value, final Object... keys ) {
+    public synchronized void put( final Object value, final Object... keys ) {
 
         Map map = this.data;
         final int keysLength = keys.length;
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
index d68e9a274..bb5516e63 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
@@ -133,12 +133,13 @@ public class VCFUtils {
             //System.out.printf("Merging in header %s%n", source);
             for ( VCFHeaderLine line : source.getMetaData()) {
                 String key = line.getKey();
+
                 if ( line instanceof VCFNamedHeaderLine )
                     key = key + "." + ((VCFNamedHeaderLine) line).getName();
 
                 if ( map.containsKey(key) ) {
                     VCFHeaderLine other = map.get(key);
-                    if ( line.equals(other) )
+                    if ( line.equals(other) || line.getVersion() != VCFHeaderVersion.VCF4_0 ) // todo -- remove me when everything is 4
                         continue;
                     else if ( ! line.getClass().equals(other.getClass()) )
                         throw new IllegalStateException("Incompatible header types: " + line + " " + other );
@@ -172,7 +173,7 @@ public class VCFUtils {
                         if ( logger != null ) logger.warn(String.format("Ignoring header line already in map: this header line = " + line + " already present header = " + other));
                     }
                 } else {
-                    line.setVersion(VCFHeaderVersion.VCF4_0);
+                    line.setVersion(VCFHeaderVersion.VCF4_0); // todo -- remove this when we finally have vcf3/4 unified headers
                     map.put(key, line);
                     //System.out.printf("Adding header line %s%n", line);
                 }
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 61744e0bc..ff828f071 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -22,28 +22,30 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
         e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "596a9ec9cbc1da70481e45a5a588a41d" );
         e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "507dbd3ba6f54e066d04c4d24f59c3ab" );
 
-        for ( Map.Entry<String, String> entry : e.entrySet() ) {
-            String bam = entry.getKey();
-            String md5 = entry.getValue();
+        for ( String parallelism : Arrays.asList("") ) { // todo -- enable parallel tests.  They work but there's a system bug Arrays.asList("", " -nt 4")) {
+            for ( Map.Entry<String, String> entry : e.entrySet() ) {
+                String bam = entry.getKey();
+                String md5 = entry.getValue();
 
-            WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                    "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
-                            " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
-                            " -T CountCovariates" +
-                            " -I " + bam +
-                            ( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" )
-                                ? " -L 1:10,800,000-10,810,000" : " -L 1:10,000,000-10,200,000" ) +
-                            " -cov ReadGroupCovariate" +
-                            " -cov QualityScoreCovariate" +
-                            " -cov CycleCovariate" +
-                            " -cov DinucCovariate" +
-                            " -cov TileCovariate" +
-                            " --solid_recal_mode SET_Q_ZERO" +
-                            " -recalFile %s",
-                    1, // just one output file
-                    Arrays.asList(md5));
-            List<File> result = executeTest("testCountCovariates1", spec).getFirst();
-            paramsFiles.put(bam, result.get(0).getAbsolutePath());
+                WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                        "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                                " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
+                                " -T CountCovariates" +
+                                " -I " + bam +
+                                ( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" )
+                                        ? " -L 1:10,800,000-10,810,000" : " -L 1:10,000,000-10,200,000" ) +
+                                " -cov ReadGroupCovariate" +
+                                " -cov QualityScoreCovariate" +
+                                " -cov CycleCovariate" +
+                                " -cov DinucCovariate" +
+                                " -cov TileCovariate" +
+                                " --solid_recal_mode SET_Q_ZERO" +
+                                " -recalFile %s" + parallelism,
+                        1, // just one output file
+                        Arrays.asList(md5));
+                List<File> result = executeTest("testCountCovariates1" + parallelism, spec).getFirst();
+                paramsFiles.put(bam, result.get(0).getAbsolutePath());
+            }
         }
     }
     
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
index 016fac9cc..0f7243ef0 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
@@ -8,8 +8,7 @@ import java.util.ArrayList;
 
 public class RecalibrationWalkersPerformanceTest extends WalkerTest {
 
-    @Test
-    public void testCountCovariatesWholeGenome() {
+    private void testCountCovariatesWholeGenomeRunner(String moreArgs) {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
                         " -T CountCovariates" +
@@ -17,14 +16,13 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
                         " -L chr1:1-50,000,000" +
                         " -standard" +
                         " -OQ" +
-                        " -recalFile /dev/null",
+                        " -recalFile /dev/null" + moreArgs,
                 0,
                 new ArrayList<String>(0));
         executeTest("testCountCovariatesWholeGenome", spec);
     }
 
-    @Test
-    public void testCountCovariatesWholeExome() {
+    private  void testCountCovariatesWholeExomeRunner(String moreArgs) {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
                         " -T CountCovariates" +
@@ -32,12 +30,22 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
                         " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
                         " -standard" +
                         " -OQ" +
-                        " -recalFile /dev/null",
+                        " -recalFile /dev/null" + moreArgs,
                 0,
                 new ArrayList<String>(0));
         executeTest("testCountCovariatesWholeExome", spec);
     }
 
+    @Test
+    public void testCountCovariatesWholeGenome() { testCountCovariatesWholeGenomeRunner(""); }
+    @Test
+    public void testCountCovariatesWholeGenomeParallel() { testCountCovariatesWholeGenomeRunner(" -nt 4"); }
+
+    @Test
+    public void testCountCovariatesWholeExome() { testCountCovariatesWholeExomeRunner(""); }
+    @Test
+    public void testCountCovariatesWholeExomeParallel() { testCountCovariatesWholeExomeRunner(" -nt 4"); }
+
     @Test
     public void testTableRecalibratorWholeGenome() {
         WalkerTestSpec spec = new WalkerTestSpec(
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
index 3d7a34b56..c82aa13ac 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -29,7 +29,7 @@ public class
         String extraArgs = "-L 1:1-10,000,000";
         for (String tests : testsEnumerations) {
             WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -o %s",
-                    1, Arrays.asList("97d2471ed6ee79d70ce5bd9cc0be2239"));
+                    1, Arrays.asList("119601d7e9e67a1053663b2e546250ed"));
             executeTest("testSelect1", spec);
         }
     }
@@ -38,7 +38,7 @@ public class
     public void testSelect2() {
         String extraArgs = "-L 1:1-10,000,000";
         WalkerTestSpec spec = new WalkerTestSpec( withSelect(withSelect(root, "DP < 50", "DP50"), "set==\"Intersection\"", "intersection") + " " + extraArgs + " -o %s",
-                1, Arrays.asList("e3366d73ee7cdf630c29809ce230e32e"));
+                1, Arrays.asList("06d495ab8169a2570eebdc54ecdffe10"));
         executeTest("testSelect2", spec);
     }
 
@@ -48,7 +48,7 @@ public class
         for (String vcfFile : vcfFiles) {
             WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B eval,VCF," + validationDataLocation + vcfFile + " -B comp,VCF," + validationDataLocation + "GenotypeConcordanceComp.vcf -E GenotypeConcordance -reportType CSV -o %s",
                     1,
-                    Arrays.asList("51574b4ab0b381c5a01268f91e78b25c"));
+                    Arrays.asList("15d1075d384da2bb7445f7493f2b6a07"));
             executeTest("testVEGenotypeConcordance" + vcfFile, spec);
         }
 
@@ -57,8 +57,8 @@ public class
     @Test
     public void testVESimple() {
         HashMap<String, String> expectations = new HashMap<String, String>();
-        expectations.put("-L 1:1-10,000,000", "8f76d8c0e3a8a5836bb5bf423e04c268");
-        expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "6b128bacbd0402471bd6d4e3f9283c47");
+        expectations.put("-L 1:1-10,000,000", "629b8b124306435ff56b66357354dfbc");
+        expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "f51c299d500b347d098c7ab25f54a436");
 
         for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
             String extraArgs = entry.getKey();
@@ -80,10 +80,10 @@ public class
                 " -B comp_hapmap,VCF," + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
 
 
-        String matchingMD5 = "aca5a64a0e4850906db2bd820253b784";
+        String matchingMD5 = "d01725ce4e46c8fea0855a923c1598fd";
         expectations.put("", matchingMD5);
         expectations.put(" -known comp_hapmap -known dbsnp", matchingMD5);
-        expectations.put(" -known comp_hapmap", "442213609c2866f7a90cbc4b3486441a");
+        expectations.put(" -known comp_hapmap", "a50be9240f6c90503fb6333d8a78b974");
         for (String tests : testsEnumerations) {
             for (Map.Entry<String, String> entry : expectations.entrySet()) {
                 String extraArgs2 = entry.getKey();
@@ -118,7 +118,7 @@ public class
         for (String tests : testsEnumerations) {
             WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs + " -o %s -outputVCF %s",
                     2,
-                    Arrays.asList("dc53aaf7db9f05e3b0a38bf5efe3fbbe", "d94328f4a5f7c40e95edf2ef13f38ae0"));
+                    Arrays.asList("483f821ce96f4cf571e9bba356c9f325", "d94328f4a5f7c40e95edf2ef13f38ae0"));
             executeTest("testVEWriteVCF", spec);
         }
     }