diff --git a/java/src/org/broadinstitute/sting/commandline/Tags.java b/java/src/org/broadinstitute/sting/commandline/Tags.java
index ec4538281..5b1e48ce9 100644
--- a/java/src/org/broadinstitute/sting/commandline/Tags.java
+++ b/java/src/org/broadinstitute/sting/commandline/Tags.java
@@ -83,6 +83,15 @@ public class Tags {
         return keyValueTags.get(key);
     }
 
+    /**
+     * Returns true if tags contains given key
+     * @param key The key for which to check existence.
+     * @return true if tags contains given key
+     */
+    public boolean containsKey(final String key) {
+        return keyValueTags.containsKey(key);
+    }
+
     /**
      * Adds positional tag(s) to the tag object.
      * @param tags The tag strings to add.
diff --git a/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java b/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
index 8d4fdd978..5a1f3378e 100644
--- a/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
+++ b/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
@@ -238,7 +238,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
         Collection<RMDTriplet> rodBindings = new ArrayList<RMDTriplet>();
 
         for (String fileName: argCollection.RODBindings) {
-            Tags tags = parser.getTags(fileName);
+            final Tags tags = parser.getTags(fileName);
             fileName = expandFileName(fileName);
 
             List<String> positionalTags = tags.getPositionalTags();
@@ -259,17 +259,18 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
             else
                 storageType = RMDStorageType.FILE;
 
-            rodBindings.add(new RMDTriplet(name,type,fileName,storageType));
+            rodBindings.add(new RMDTriplet(name,type,fileName,storageType,tags));
         }
 
         if (argCollection.DBSNPFile != null) {
             if(argCollection.DBSNPFile.toLowerCase().contains("vcf"))
                 throw new UserException("--DBSNP (-D) argument currently does not support VCF.  To use dbSNP in VCF format, please use -B:dbsnp,vcf <filename>.");
 
+            final Tags tags = parser.getTags(argCollection.DBSNPFile);
             String fileName = expandFileName(argCollection.DBSNPFile);
             RMDStorageType storageType = fileName.toLowerCase().endsWith("stdin") ? RMDStorageType.STREAM : RMDStorageType.FILE;
 
-            rodBindings.add(new RMDTriplet(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME,"dbsnp",fileName,storageType));
+            rodBindings.add(new RMDTriplet(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME,"dbsnp",fileName,storageType,tags));
         }
 
         return rodBindings;
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java
index 4680c003a..60b68bda5 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java
@@ -25,6 +25,7 @@
 package org.broadinstitute.sting.gatk.datasources.rmd;
 
 import net.sf.samtools.SAMSequenceDictionary;
+import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
 import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
@@ -124,6 +125,15 @@ public class ReferenceOrderedDataSource {
         return header;
     }
 
+    public Tags getTags() {
+        return fileDescriptor.getTags();
+    }
+    
+    public String getTagValue( final String key ) {
+        return fileDescriptor.getTags().getValue( key );
+    }
+
+
     /**
      * Retrieves the sequence dictionary created by this ROD.
      * @return
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java
index 23063ee16..c2057ad5e 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java
@@ -33,6 +33,7 @@ import org.broad.tribble.index.Index;
 import org.broad.tribble.index.IndexFactory;
 import org.broad.tribble.source.BasicFeatureSource;
 import org.broad.tribble.util.LittleEndianOutputStream;
+import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
@@ -168,7 +169,7 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
         if(typeName == null)
             throw new ReviewedStingException("Unable to find type name for class " + targetClass.getName());
 
-        return createInstanceOfTrack(new RMDTriplet("anonymous",typeName,inputFile.getAbsolutePath(),RMDStorageType.FILE));
+        return createInstanceOfTrack(new RMDTriplet("anonymous",typeName,inputFile.getAbsolutePath(),RMDStorageType.FILE,new Tags()));
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/utils/RMDTriplet.java b/java/src/org/broadinstitute/sting/gatk/refdata/utils/RMDTriplet.java
index 3f23d94c8..72c345d0f 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/utils/RMDTriplet.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/utils/RMDTriplet.java
@@ -24,6 +24,8 @@
 package org.broadinstitute.sting.gatk.refdata.utils;
 
 
+import org.broadinstitute.sting.commandline.Tags;
+
 /**
  * a helper class to manage our triplets of data for the -B command line option (name, type, file)
  * TODO: The presence of four datapoints here suggests that this class' name isn't sufficient to describe its function.  Rename.
@@ -35,12 +37,14 @@ public class RMDTriplet {
     private final String type;
     private final String file;
     private final RMDStorageType storageType;
+    private final Tags tags;
 
-    public RMDTriplet(final String name, final String type, final String file, final RMDStorageType storageType) {
+    public RMDTriplet(final String name, final String type, final String file, final RMDStorageType storageType, final Tags tags) {
         this.name = name;
         this.type = type;
         this.file = file;
         this.storageType = storageType;
+        this.tags = tags;
     }
 
     /**
@@ -75,4 +79,12 @@ public class RMDTriplet {
     public RMDStorageType getStorageType() {
         return storageType;
     }
+
+    /**
+     * Gets the key=value tags associated with this track
+     * @return Tags associated with this track.
+     */
+    public Tags getTags() {
+        return tags;
+    }
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
index e74f0732b..b20fbbe59 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
@@ -54,7 +54,6 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
     /////////////////////////////
     // Outputs
     /////////////////////////////
-
     @Output(fullName="cluster_file", shortName="clusterFile", doc="The output cluster file", required=true)
     private PrintStream CLUSTER_FILE;
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ApplyRecalibration.java
index 77ef59ca0..ac487a7af 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ApplyRecalibration.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ApplyRecalibration.java
@@ -74,15 +74,18 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
     /////////////////////////////
     // Command Line Arguments
     /////////////////////////////
-    @Argument(fullName="fdr_filter_level", shortName="fdr_filter_level", doc="The FDR level at which to start filtering.", required=false)
-    private double FDR_FILTER_LEVEL = 1.0;
-    
+    @Argument(fullName="ts_filter_level", shortName="ts_filter_level", doc="The truth sensitivity level at which to start filtering", required=false)
+    private double TS_FILTER_LEVEL = 99.0;
+    @Argument(fullName="ignore_filter", shortName="ignoreFilter", doc="If specified the optimizer will use variants even if the specified filter name is marked in the input VCF file", required=false)
+    private String[] IGNORE_INPUT_FILTERS = null;
+
     /////////////////////////////
     // Private Member Variables
     /////////////////////////////
     final private List<Tranche> tranches = new ArrayList<Tranche>();
     final private Set<String> inputNames = new HashSet<String>();
     final private NestedHashMap lodMap = new NestedHashMap();
+    final private Set<String> ignoreInputFilterSet = new TreeSet<String>();
 
     //---------------------------------------------------------------------------------------------------------------
     //
@@ -92,13 +95,12 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
 
     public void initialize() {
         for ( final Tranche t : Tranche.readTranches(TRANCHES_FILE) ) {
-            if ( t.fdr >= FDR_FILTER_LEVEL) {
+            if ( t.ts >= TS_FILTER_LEVEL ) {
                 tranches.add(t);
-                //statusMsg = "Keeping, above FDR threshold";
             }
             logger.info(String.format("Read tranche " + t));
         }
-        Collections.reverse(tranches); // this algorithm wants the tranches ordered from worst to best
+        Collections.reverse(tranches); // this algorithm wants the tranches ordered from best (lowest truth sensitivity) to worst (highest truth sensitivity)
 
         for( final ReferenceOrderedDataSource d : this.getToolkit().getRodDataSources() ) {
             if( d.getName().startsWith("input") ) {
@@ -113,6 +115,10 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
             throw new UserException.BadInput( "No input variant tracks found. Input variant binding names must begin with 'input'." );
         }
 
+        if( IGNORE_INPUT_FILTERS != null ) {
+            ignoreInputFilterSet.addAll( Arrays.asList(IGNORE_INPUT_FILTERS) );
+        }
+
         // setup the header fields
         final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
@@ -122,14 +128,14 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
 
         if( tranches.size() >= 2 ) {
             for( int iii = 0; iii < tranches.size() - 1; iii++ ) {
-                Tranche t = tranches.get(iii);
-                hInfo.add(new VCFFilterHeaderLine(t.name, String.format("FDR tranche level at VSQ Lod: " + t.minVQSLod + " <= x < " + tranches.get(iii+1).minVQSLod)));
+                final Tranche t = tranches.get(iii);
+                hInfo.add(new VCFFilterHeaderLine(t.name, String.format("Truth sensitivity tranche level at VSQ Lod: " + t.minVQSLod + " <= x < " + tranches.get(iii+1).minVQSLod)));
             }
         }
         if( tranches.size() >= 1 ) {
-            hInfo.add(new VCFFilterHeaderLine(tranches.get(0).name + "+", String.format("FDR tranche level at VQS Lod < " + tranches.get(0).minVQSLod)));
+            hInfo.add(new VCFFilterHeaderLine(tranches.get(0).name + "+", String.format("Truth sensitivity tranche level at VQS Lod < " + tranches.get(0).minVQSLod)));
         } else {
-            throw new UserException("No tranches were found in the file or were above the FDR Filter level " + FDR_FILTER_LEVEL);
+            throw new UserException("No tranches were found in the file or were above the truth sensitivity filter level " + TS_FILTER_LEVEL);
         }
 
         logger.info("Keeping all variants in tranche " + tranches.get(tranches.size()-1));
@@ -141,7 +147,7 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
             logger.info("Reading in recalibration table...");
             for ( final String line : new XReadLines( RECAL_FILE ) ) {
                 final String[] vals = line.split(",");
-                lodMap.put( Double.parseDouble(vals[2]), vals[0], Integer.parseInt(vals[1]));
+                lodMap.put( Double.parseDouble(vals[3]), vals[0], Integer.parseInt(vals[1]), Integer.parseInt(vals[2]) ); // value comes before the keys
             }
         } catch ( FileNotFoundException e ) {
             throw new UserException.CouldNotReadInputFile(RECAL_FILE, e);
@@ -164,38 +170,31 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
         for( VariantContext vc : tracker.getVariantContexts(ref, inputNames, null, context.getLocation(), true, false) ) {
             if( vc != null ) {
                 String filterString = null;
-                final Double lod = (Double) lodMap.get( ref.getLocus().getContig(), ref.getLocus().getStart() );
-                if( !vc.isFiltered() ) {
-                    try {
-                        for( int i = tranches.size() - 1; i >= 0; i-- ) {
-                            final Tranche tranche = tranches.get(i);
-                            if( lod >= tranche.minVQSLod ) {
-                                if (i == tranches.size() - 1) {
-                                    filterString = VCFConstants.PASSES_FILTERS_v4;
-                                } else {
-                                    filterString = tranche.name;
-                                }
-                                break;
-                            }
-                        }
-
-                        if( filterString == null ) {
-                            filterString = tranches.get(0).name+"+";
-                        }
-
-                        if ( !filterString.equals(VCFConstants.PASSES_FILTERS_v4) ) {
-                            final Set<String> filters = new HashSet<String>();
-                            filters.add(filterString);
-                            vc = VariantContext.modifyFilters(vc, filters);
-                        }
-                    } catch ( Exception e ) {
-                        throw new UserException.MalformedFile(vc.getSource(), "Invalid value for VQS key " + ContrastiveRecalibrator.VQS_LOD_KEY + " at variant " + vc, e);
-                    }
-                }
-
                 final Map<String, Object> attrs = new HashMap<String, Object>(vc.getAttributes());
-                if(lod != null) {
+                final Double lod = (Double) lodMap.get( ref.getLocus().getContig(), ref.getLocus().getStart(), ref.getLocus().getStop() );
+                if( vc.isNotFiltered() || ignoreInputFilterSet.containsAll(vc.getFilters()) ) {
                     attrs.put(ContrastiveRecalibrator.VQS_LOD_KEY, String.format("%.4f", lod));
+                    for( int i = tranches.size() - 1; i >= 0; i-- ) {
+                        final Tranche tranche = tranches.get(i);
+                        if( lod >= tranche.minVQSLod ) {
+                            if( i == tranches.size() - 1 ) {
+                                filterString = VCFConstants.PASSES_FILTERS_v4;
+                            } else {
+                                filterString = tranche.name;
+                            }
+                            break;
+                        }
+                    }
+
+                    if( filterString == null ) {
+                        filterString = tranches.get(0).name+"+";
+                    }
+
+                    if( !filterString.equals(VCFConstants.PASSES_FILTERS_v4) ) {
+                        final Set<String> filters = new HashSet<String>();
+                        filters.add(filterString);
+                        vc = VariantContext.modifyFilters(vc, filters);
+                    }
                 }
 
                 vcfWriter.add( VariantContext.modifyPErrorFiltersAndAttributes(vc, vc.getNegLog10PError(), vc.getFilters(), attrs), ref.getBase() );
@@ -219,7 +218,7 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
         return 1; // This value isn't used for anything
     }
 
-    public void onTraversalDone( Integer reduceSum ) {
+    public void onTraversalDone( final Integer reduceSum ) {
     }
 }
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ContrastiveRecalibrator.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ContrastiveRecalibrator.java
index cca347385..98f7ad473 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ContrastiveRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ContrastiveRecalibrator.java
@@ -36,7 +36,6 @@ import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
-import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -72,8 +71,10 @@ public class ContrastiveRecalibrator extends RodWalker<ExpandingArrayList<Varian
     //BUGBUG: use VariantRecalibrationArgumentCollection
     @Argument(fullName="use_annotation", shortName="an", doc="The names of the annotations which should used for calculations", required=true)
     private String[] USE_ANNOTATIONS = null;
-    @Argument(fullName="FDRtranche", shortName="tranche", doc="The levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)", required=false)
-    private double[] FDR_TRANCHES = new double[]{0.1, 1.0, 10.0, 100.0};
+    @Argument(fullName="TStranche", shortName="tranche", doc="The levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)", required=false)
+    private double[] TS_TRANCHES = new double[] {100.0, 99.9, 99.0, 90.0};
+    @Argument(fullName="ignore_filter", shortName="ignoreFilter", doc="If specified the optimizer will use variants even if the specified filter name is marked in the input VCF file", required=false)
+    private String[] IGNORE_INPUT_FILTERS = null;
 
     /////////////////////////////
     // Debug Arguments
@@ -85,13 +86,13 @@ public class ContrastiveRecalibrator extends RodWalker<ExpandingArrayList<Varian
     @Argument(fullName = "trustAllPolymorphic", shortName = "allPoly", doc = "Trust that all the input training sets' unfiltered records contain only polymorphic sites to drastically speed up the computation.", required = false)
     protected Boolean TRUST_ALL_POLYMORPHIC = false;
 
-
     /////////////////////////////
     // Private Member Variables
     /////////////////////////////
     private VariantDataManager dataManager;
-    private Set<String> inputNames = new HashSet<String>();
-    private VariantRecalibratorEngine engine = new VariantRecalibratorEngine(new VariantRecalibratorArgumentCollection()); //BUGBUG: doesn't do anything with the args at the moment
+    private final Set<String> ignoreInputFilterSet = new TreeSet<String>();
+    private final Set<String> inputNames = new HashSet<String>();
+    private final VariantRecalibratorEngine engine = new VariantRecalibratorEngine(new VariantRecalibratorArgumentCollection()); //BUGBUG: doesn't do anything with the args at the moment
 
     //---------------------------------------------------------------------------------------------------------------
     //
@@ -102,35 +103,27 @@ public class ContrastiveRecalibrator extends RodWalker<ExpandingArrayList<Varian
     public void initialize() {
         dataManager = new VariantDataManager( new ArrayList<String>(Arrays.asList(USE_ANNOTATIONS)) );
 
+        if( IGNORE_INPUT_FILTERS != null ) {
+            ignoreInputFilterSet.addAll( Arrays.asList(IGNORE_INPUT_FILTERS) );
+        }
+
         for( ReferenceOrderedDataSource d : this.getToolkit().getRodDataSources() ) {
             if( d.getName().toLowerCase().startsWith("input") ) {
                 inputNames.add(d.getName());
-                logger.info("Found input variant track with name " + d.getName());
-            } else if ( d.getName().equals("dbsnp") ) { //BUGBUG: values are hard coded for now until command line tagging up for Rod bindings
-                logger.info("Found dbSNP  track: \tKnown = true \tTraining = false \tTruth = false \tPrior = Q10.0");
-                dataManager.addTrainingSet(new TrainingSet("dbsnp", true, false, false, 10.0));
-            } else if ( d.getName().equals("hapmap") ) {
-                logger.info("Found HapMap track: \tKnown = false \tTraining = true \tTruth = true \tPrior = Q12.0");
-                dataManager.addTrainingSet(new TrainingSet("hapmap", false, true, true, 12.0));
-            } else if ( d.getName().equals("1kg") ) {
-                logger.info("Found 1KG    track: \tKnown = false \tTraining = true \tTruth = false \tPrior = Q6.0");
-                dataManager.addTrainingSet(new TrainingSet("1kg", false, true, false, 6.0));
-            } else if ( d.getName().equals("omni") ) {
-                logger.info("Found Omni   track: \tKnown = false \tTraining = true \tTruth = true \tPrior = Q15.0");
-                dataManager.addTrainingSet( new TrainingSet("omni", false, true, true, 15.0) );
+                logger.info( "Found input variant track with name " + d.getName() );
             } else {
-                logger.info("WARNING! Not evaluating ROD binding: " + d.getName());
+                dataManager.addTrainingSet( new TrainingSet(d.getName(), d.getTags()) );
             }
         }
 
         if( !dataManager.checkHasTrainingSet() ) {
-            throw new UserException.CommandLineException("No training set found! Please provide sets of known polymorphic loci to be used as training data using the dbsnp, hapmap, 1kg, or omni rod bindings.");
+            throw new UserException.CommandLineException( "No training set found! Please provide sets of known polymorphic loci marked with the training=true ROD binding tag. For example, -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmapFile.vcf" );
         }
         if( !dataManager.checkHasTruthSet() ) {
-            throw new UserException.CommandLineException("No truth set found! Please provide sets of known polymorphic loci to be used as training data using the dbsnp, hapmap, 1kg, or omni rod bindings.");
+            throw new UserException.CommandLineException( "No truth set found! Please provide sets of known polymorphic loci marked with the truth=true ROD binding tag. For example, -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmapFile.vcf" );
         }
         if( !dataManager.checkHasKnownSet() ) {
-            throw new UserException.CommandLineException("No known set found! Please provide sets of known polymorphic loci to be used as training data using the dbsnp, hapmap, 1kg, or omni rod bindings.");
+            throw new UserException.CommandLineException( "No known set found! Please provide sets of known polymorphic loci marked with the known=true ROD binding tag. For example, -B:dbsnp,VCF,known=true,training=false,truth=false,prior=8.0 dbsnpFile.vcf" );
         }
 
         if( inputNames.size() == 0 ) {
@@ -152,7 +145,7 @@ public class ContrastiveRecalibrator extends RodWalker<ExpandingArrayList<Varian
         }
 
         for( final VariantContext vc : tracker.getVariantContexts(ref, inputNames, null, context.getLocation(), true, false) ) {
-            if( vc != null ) { // BUGBUG: filtered?
+            if( vc != null && ( vc.isNotFiltered() || ignoreInputFilterSet.containsAll(vc.getFilters()) ) ) {
                 final VariantDatum datum = new VariantDatum();
                 datum.annotations = dataManager.decodeAnnotations( ref.getGenomeLocParser(), vc, true ); //BUGBUG: when run with HierarchicalMicroScheduler this is non-deterministic because order of calls depends on load of machine
                 datum.pos = context.getLocation();
@@ -205,7 +198,7 @@ public class ContrastiveRecalibrator extends RodWalker<ExpandingArrayList<Varian
         //logger.info(String.format("Truth set size is %d, raw calls at these sites %d, maximum sensitivity of %.2f",
         //        nTruthSites, nCallsAtTruth, (100.0*nCallsAtTruth / Math.max(nTruthSites, nCallsAtTruth))));
         TrancheManager.SelectionMetric metric = new TrancheManager.TruthSensitivityMetric( nCallsAtTruth );
-        List<Tranche> tranches = TrancheManager.findTranches( dataManager.getData(), FDR_TRANCHES, metric, DEBUG_FILE ); //BUGBUG: recreated here to match the integration tests
+        List<Tranche> tranches = TrancheManager.findTranches( dataManager.getData(), TS_TRANCHES, metric, DEBUG_FILE ); //BUGBUG: recreated here to match the integration tests
         TRANCHES_FILE.print(Tranche.tranchesString( tranches ));
 
         logger.info( "Writing out recalibration table..." );
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/GaussianMixtureModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
index a8d00c186..ddc12269f 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
@@ -89,7 +89,7 @@ public class GaussianMixtureModel {
             gaussian.initializeRandomSigma( rand );
             gaussian.hyperParameter_a = degreesOfFreedom;
             gaussian.hyperParameter_b = shrinkage;
-            gaussian.hyperParameter_lambda = dirichletParameter;            
+            gaussian.hyperParameter_lambda = dirichletParameter;
         }
     }
 
@@ -116,7 +116,7 @@ public class GaussianMixtureModel {
                 int numAssigned = 0;
 
                 for( final VariantDatum datum : data ) {
-                    if( datum.assignment == gaussian ) {
+                    if( datum.assignment.equals(gaussian) ) {
                         numAssigned++;
                         gaussian.incrementMu( datum );
                     }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/MultivariateGaussian.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/MultivariateGaussian.java
index dae7b17b1..a3c909bf6 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/MultivariateGaussian.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/MultivariateGaussian.java
@@ -55,10 +55,10 @@ public class MultivariateGaussian {
             for( int iii = 0; iii < mu.length; iii++ ) {
                 for( int jjj = iii; jjj < mu.length; jjj++ ) {
                     randSigma[jjj][iii] = 0.55 + 1.25 * rand.nextDouble();
-                    if(rand.nextBoolean()) {
+                    if( rand.nextBoolean() ) {
                         randSigma[jjj][iii] *= -1.0;
                     }
-                    if(iii != jjj) { randSigma[iii][jjj] = 0.0; } // Sigma is a symmetric, positive-definite matrix created by taking a lower diagonal matrix and multiplying it by its transpose
+                    if( iii != jjj ) { randSigma[iii][jjj] = 0.0; } // Sigma is a symmetric, positive-definite matrix created by taking a lower diagonal matrix and multiplying it by its transpose
                 }
             }
         Matrix tmp = new Matrix( randSigma );
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrainingSet.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrainingSet.java
index 49bc1e923..8e12cf544 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrainingSet.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrainingSet.java
@@ -1,28 +1,32 @@
 package org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration;
 
+import org.apache.log4j.Logger;
+import org.broadinstitute.sting.commandline.Tags;
+
 /**
  * Created by IntelliJ IDEA.
  * User: rpoplin
  * Date: 3/12/11
  */
 
-public class TrainingSet implements Comparable<TrainingSet> {
+public class TrainingSet {
 
     public String name;
-    public boolean isKnown;
-    public boolean isTraining;
-    public boolean isTruth;
-    public double prior;
+    public boolean isKnown = false;
+    public boolean isTraining = false;
+    public boolean isTruth = false;
+    public double prior = 3.0;
 
-    public TrainingSet( final String name, final boolean isKnown, final boolean isTraining, final boolean isTruth, final double prior ) {
+    protected final static Logger logger = Logger.getLogger(TrainingSet.class);
+
+    public TrainingSet( final String name, final Tags tags ) {
         this.name = name;
-        this.isKnown = isKnown;
-        this.isTraining = isTraining;
-        this.isTruth = isTruth;
-        this.prior = prior;
-    }
-
-    public int compareTo( final TrainingSet other ) {
-        return Double.compare(this.prior, other.prior);
+        if( tags != null ) {
+            isKnown = tags.containsKey("known") && tags.getValue("known").equals("true");
+            isTraining = tags.containsKey("training") && tags.getValue("training").equals("true");
+            isTruth = tags.containsKey("truth") && tags.getValue("truth").equals("true");
+            prior = ( tags.containsKey("known") ? Double.parseDouble(tags.getValue("prior")) : prior );
+        }
+        logger.info(String.format( "Found %s track: \tKnown = %s \tTraining = %s \tTruth = %s \tPrior = Q%.1f", this.name, isKnown, isTraining, isTruth, prior) );
     }
 }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/Tranche.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/Tranche.java
index f3ea7ad92..b685c9e68 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/Tranche.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/Tranche.java
@@ -39,22 +39,21 @@ import java.util.*;
  */
 
 public class Tranche implements Comparable<Tranche> {
-    private static final int CURRENT_VERSION = 3;
+    private static final int CURRENT_VERSION = 4;
 
-    public double fdr, minVQSLod, targetTiTv, knownTiTv, novelTiTv;
+    public double ts, minVQSLod, knownTiTv, novelTiTv;
     public int numKnown,numNovel;
     public String name;
 
     int accessibleTruthSites = 0;
     int callsAtTruthSites = 0;
 
-    public Tranche(double fdr, double targetTiTv, double minVQSLod, int numKnown, double knownTiTv, int numNovel, double novelTiTv, int accessibleTruthSites, int callsAtTruthSites) {
-        this(fdr, targetTiTv, minVQSLod, numKnown, knownTiTv, numNovel, novelTiTv, accessibleTruthSites, callsAtTruthSites, "anonymous");
+    public Tranche(double ts, double minVQSLod, int numKnown, double knownTiTv, int numNovel, double novelTiTv, int accessibleTruthSites, int callsAtTruthSites) {
+        this(ts, minVQSLod, numKnown, knownTiTv, numNovel, novelTiTv, accessibleTruthSites, callsAtTruthSites, "anonymous");
     }
 
-    public Tranche(double fdr, double targetTiTv, double minVQSLod, int numKnown, double knownTiTv, int numNovel, double novelTiTv, int accessibleTruthSites, int callsAtTruthSites, String name ) {
-        this.fdr = fdr;
-        this.targetTiTv = targetTiTv;
+    public Tranche(double ts, double minVQSLod, int numKnown, double knownTiTv, int numNovel, double novelTiTv, int accessibleTruthSites, int callsAtTruthSites, String name ) {
+        this.ts = ts;
         this.minVQSLod = minVQSLod;
         this.novelTiTv = novelTiTv;
         this.numNovel = numNovel;
@@ -65,11 +64,8 @@ public class Tranche implements Comparable<Tranche> {
         this.accessibleTruthSites = accessibleTruthSites;
         this.callsAtTruthSites = callsAtTruthSites;
 
-        if ( fdr < 0.0 )
-            throw new UserException("Target FDR is unreasonable " + fdr);
-
-        if ( targetTiTv < 0.5 || targetTiTv > 10 )
-            throw new UserException("Target Ti/Tv ratio is unreasonable " + targetTiTv);
+        if ( ts < 0.0 || ts > 100.0)
+            throw new UserException("Target FDR is unreasonable " + ts);
 
         if ( numKnown < 0 || numNovel < 0)
             throw new ReviewedStingException("Invalid tranche - no. variants is < 0 : known " + numKnown + " novel " + numNovel);
@@ -83,37 +79,35 @@ public class Tranche implements Comparable<Tranche> {
     }
 
     public int compareTo(Tranche other) {
-        return Double.compare(this.fdr,  other.fdr);
+        return Double.compare(this.ts,  other.ts);
     }
 
     public String toString() {
-        return String.format("Tranche fdr=%.2f minVQSLod=%.4f known=(%d @ %.2f) novel=(%d @ %.2f) truthSites(%d accessible, %d called), name=%s]",
-                fdr, minVQSLod, numKnown, knownTiTv, numNovel, novelTiTv, accessibleTruthSites, callsAtTruthSites, name);
+        return String.format("Tranche ts=%.2f minVQSLod=%.4f known=(%d @ %.2f) novel=(%d @ %.2f) truthSites(%d accessible, %d called), name=%s]",
+                ts, minVQSLod, numKnown, knownTiTv, numNovel, novelTiTv, accessibleTruthSites, callsAtTruthSites, name);
     }
 
     /**
      * Returns an appropriately formatted string representing the raw tranches file on disk.
      *
-     * @param rawTranches
+     * @param tranches
      * @return
      */
-    public static String tranchesString(List<Tranche> rawTranches) {
-        ByteArrayOutputStream bytes = new ByteArrayOutputStream();
-        PrintStream stream = new PrintStream(bytes);
+    public static String tranchesString( final List<Tranche> tranches ) {
+        final ByteArrayOutputStream bytes = new ByteArrayOutputStream();
+        final PrintStream stream = new PrintStream(bytes);
 
-        List<Tranche> tranches = new ArrayList<Tranche>();
-        tranches.addAll(rawTranches);
         Collections.sort(tranches);
 
         stream.println("# Variant quality score tranches file");
         stream.println("# Version number " + CURRENT_VERSION);
-        stream.println("FDRtranche,targetTiTv,numKnown,numNovel,knownTiTv,novelTiTv,minVQSLod,filterName,accessibleTruthSites,callsAtTruthSites,truthSensitivity");
+        stream.println("targetTruthSensitivity,numKnown,numNovel,knownTiTv,novelTiTv,minVQSLod,filterName,accessibleTruthSites,callsAtTruthSites,truthSensitivity");
 
         Tranche prev = null;
         for ( Tranche t : tranches ) {
-            stream.printf("%.2f,%.2f,%d,%d,%.4f,%.4f,%.4f,FDRtranche%.2fto%.2f,%d,%d,%.4f%n",
-                    t.fdr,t.targetTiTv,t.numKnown,t.numNovel,t.knownTiTv,t.novelTiTv, t.minVQSLod,
-                    (prev == null ? 0.0 : prev.fdr), t.fdr, t.accessibleTruthSites, t.callsAtTruthSites, t.getTruthSensitivity());
+            stream.printf("%.2f,%d,%d,%.4f,%.4f,%.4f,TruthSensitivityTranche%.2fto%.2f,%d,%d,%.4f%n",
+                    t.ts, t.numKnown, t.numNovel, t.knownTiTv, t.novelTiTv, t.minVQSLod,
+                    (prev == null ? 0.0 : prev.ts), t.ts, t.accessibleTruthSites, t.callsAtTruthSites, t.getTruthSensitivity());
             prev = t;
         }
 
@@ -160,19 +154,18 @@ public class Tranche implements Comparable<Tranche> {
                 final String[] vals = line.split(",");
                 if( header == null ) {
                     header = vals;
-                    if ( header.length == 5 )
+                    if ( header.length == 5 || header.length == 8 || header.length == 11 )
                         // old style tranches file, throw an error
                         throw new UserException.MalformedFile(f, "Unfortunately, your tranches file is from a previous version of this tool and cannot be used with the latest code.  Please rerun VariantRecalibrator");
-                    if ( header.length != 8 && header.length != 11 )
-                        throw new UserException.MalformedFile(f, "Expected 8 elements in header line " + line);
+                    if ( header.length != 10 )
+                        throw new UserException.MalformedFile(f, "Expected 10 elements in header line " + line);
                 } else {
                     if ( header.length != vals.length )
                         throw new UserException.MalformedFile(f, "Line had too few/many fields.  Header = " + header.length + " vals " + vals.length + " line " + line);
 
                     Map<String,String> bindings = new HashMap<String, String>();
                     for ( int i = 0; i < vals.length; i++ ) bindings.put(header[i], vals[i]);
-                    tranches.add(new Tranche(getDouble(bindings,"FDRtranche", true),
-                            getDouble(bindings,"targetTiTv", false),
+                    tranches.add(new Tranche(getDouble(bindings,"targetTruthSensitivity", true),
                             getDouble(bindings,"minVQSLod", true),
                             getInteger(bindings,"numKnown", false),
                             getDouble(bindings,"knownTiTv", false),
@@ -184,7 +177,7 @@ public class Tranche implements Comparable<Tranche> {
                 }
             }
 
-            Collections.sort(tranches);   // sort this in the standard order
+            Collections.sort(tranches);
             return tranches;
         } catch( FileNotFoundException e ) {
             throw new UserException.CouldNotReadInputFile(f, e);
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrancheManager.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrancheManager.java
index cd8c60cce..49b464eda 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrancheManager.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/TrancheManager.java
@@ -91,7 +91,7 @@ public class TrancheManager {
         }
 
         public double getThreshold(double tranche) {
-            return tranche/100; // tranche of 1 => 99% sensitivity target
+            return 1.0 - tranche/100.0; // tranche of 1 => 99% sensitivity target
         }
 
         public double getTarget() { return 1.0; }
@@ -123,14 +123,14 @@ public class TrancheManager {
     public static List<Tranche> findTranches( ArrayList<VariantDatum> data, final double[] trancheThresholds, SelectionMetric metric, File debugFile ) {
         logger.info(String.format("Finding %d tranches for %d variants", trancheThresholds.length, data.size()));
 
-        List<VariantDatum> tranchesData = sortVariantsbyLod(data);
-        metric.calculateRunningMetric(tranchesData);
+        Collections.sort(data);
+        metric.calculateRunningMetric(data);
 
-        if ( debugFile != null) { writeTranchesDebuggingInfo(debugFile, tranchesData, metric); }
+        if ( debugFile != null) { writeTranchesDebuggingInfo(debugFile, data, metric); }
 
         List<Tranche> tranches = new ArrayList<Tranche>();
         for ( double trancheThreshold : trancheThresholds ) {
-            Tranche t = findTranche(tranchesData, metric, trancheThreshold);
+            Tranche t = findTranche(data, metric, trancheThreshold);
 
             if ( t == null ) {
                 if ( tranches.size() == 0 )
@@ -159,11 +159,6 @@ public class TrancheManager {
         }
     }
 
-    private static List<VariantDatum> sortVariantsbyLod(final ArrayList<VariantDatum> data) {
-        Collections.sort(data);
-        return data;
-    }
-
     public static Tranche findTranche( final List<VariantDatum> data, final SelectionMetric metric, final double trancheThreshold ) {
         logger.info(String.format("  Tranche threshold %.2f => selection metric threshold %.3f", trancheThreshold, metric.getThreshold(trancheThreshold)));
 
@@ -171,8 +166,8 @@ public class TrancheManager {
         int n = data.size();
         for ( int i = 0; i < n; i++ ) {
             if ( metric.getRunningMetric(i) >= metricThreshold ) {
-                // we've found the largest group of variants with Ti/Tv >= our target titv
-                Tranche t = trancheOfVariants(data, i, trancheThreshold, metric.getTarget());
+                // we've found the largest group of variants with sensitivity >= our target truth sensitivity
+                Tranche t = trancheOfVariants(data, i, trancheThreshold);
                 logger.info(String.format("  Found tranche for %.3f: %.3f threshold starting with variant %d; running score is %.3f ",
                         trancheThreshold, metricThreshold, i, metric.getRunningMetric(i)));
                 logger.info(String.format("  Tranche is %s", t));
@@ -183,7 +178,7 @@ public class TrancheManager {
         return null;
     }
 
-    public static Tranche trancheOfVariants( final List<VariantDatum> data, int minI, double fdr, double target ) {
+    public static Tranche trancheOfVariants( final List<VariantDatum> data, int minI, double ts ) {
         int numKnown = 0, numNovel = 0, knownTi = 0, knownTv = 0, novelTi = 0, novelTv = 0;
 
         double minLod = data.get(minI).lod;
@@ -207,7 +202,7 @@ public class TrancheManager {
         int accessibleTruthSites = countCallsAtTruth(data, Double.NEGATIVE_INFINITY);
         int nCallsAtTruth = countCallsAtTruth(data, minLod);
 
-        return new Tranche(fdr, target, minLod, numKnown, knownTiTv, numNovel, novelTiTv, accessibleTruthSites, nCallsAtTruth);
+        return new Tranche(ts, minLod, numKnown, knownTiTv, numNovel, novelTiTv, accessibleTruthSites, nCallsAtTruth);
     }
 
     public static double fdrToTiTv(double desiredFDR, double targetTiTv) {
@@ -216,7 +211,7 @@ public class TrancheManager {
 
     public static int countCallsAtTruth(final List<VariantDatum> data, double minLOD ) {
         int n = 0;
-        for ( VariantDatum d : data) { n += d.atTruthSite && d.lod >= minLOD ? 1 : 0; }
+        for ( VariantDatum d : data) { n += (d.atTruthSite && d.lod >= minLOD ? 1 : 0); }
         return n;
     }
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantDataManager.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantDataManager.java
index 4cfd4e325..507cda88a 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -27,7 +27,7 @@ public class VariantDataManager {
     private final ExpandingArrayList<TrainingSet> trainingSets;
 
     private final static long RANDOM_SEED = 83409701;
-    private final static Random rand = new Random( RANDOM_SEED ); // this is going to cause problems if it is ever used in an integration test
+    private final static Random rand = new Random( RANDOM_SEED ); // this is going to cause problems if it is ever used in an integration test, planning to get rid of HRun anyway
 
     protected final static Logger logger = Logger.getLogger(VariantDataManager.class);
 
@@ -53,11 +53,7 @@ public class VariantDataManager {
             final double theMean = mean(jjj); //BUGBUG: to clean up
             final double theSTD = standardDeviation(theMean, jjj); //BUGBUG: to clean up
             logger.info( annotationKeys.get(jjj) + String.format(": \t mean = %.2f\t standard deviation = %.2f", theMean, theSTD) );
-            if( theSTD < 1E-8 ) { //BUGBUG: output recreated here to match the integration tests
-                foundZeroVarianceAnnotation = true;
-            } else if( theSTD < 1E-2 ) {
-                logger.warn("Warning! Tiny variance. It is strongly recommended that you -exclude " + annotationKeys.get(jjj));
-            }
+            foundZeroVarianceAnnotation = foundZeroVarianceAnnotation || (theSTD < 1E-8);
             meanVector[jjj] = theMean;
             varianceVector[jjj] = theSTD;
             for( final VariantDatum datum : data ) {
@@ -65,7 +61,7 @@ public class VariantDataManager {
             }
         }
         if( foundZeroVarianceAnnotation ) {
-            throw new UserException.BadInput("Found annotations with zero variance. They must be excluded before proceeding.");
+            throw new UserException.BadInput( "Found annotations with zero variance. They must be excluded before proceeding." );
         }
     }
 
@@ -136,7 +132,7 @@ public class VariantDataManager {
         final ExpandingArrayList<VariantDatum> dataToRemove = new ExpandingArrayList<VariantDatum>();
         for( final VariantDatum datum : listData ) {
             boolean remove = false;
-            for( double val : datum.annotations ) {
+            for( final double val : datum.annotations ) {
                 remove = remove || (Math.abs(val) > STD_THRESHOLD);
             }
             if( remove ) { dataToRemove.add( datum ); }
@@ -163,8 +159,8 @@ public class VariantDataManager {
         } else {
             try {
                 value = Double.parseDouble( (String)vc.getAttribute( annotationKey ) );
-            } catch( Exception e ) {
-                throw new UserException.MalformedFile(vc.getSource(), "No double value detected for annotation = " + annotationKey + " in variant at " + VariantContextUtils.getLocation(genomeLocParser,vc) + ", reported annotation value = " + vc.getAttribute( annotationKey ), e );
+            } catch( final Exception e ) {
+                throw new UserException.MalformedFile( vc.getSource(), "No double value detected for annotation = " + annotationKey + " in variant at " + VariantContextUtils.getLocation(genomeLocParser,vc) + ", reported annotation value = " + vc.getAttribute( annotationKey ), e );
             }
         }
         return value;
@@ -188,8 +184,8 @@ public class VariantDataManager {
     }
 
     public void writeOutRecalibrationTable( final PrintStream RECAL_FILE ) {
-        for( final VariantDatum datum : data ) { //BUGBUG: quick and dirty for now, only works for SNPs.
-            RECAL_FILE.println(String.format("%s,%d,%.4f", datum.pos.getContig(), datum.pos.getStart(), datum.lod));
+        for( final VariantDatum datum : data ) {
+            RECAL_FILE.println(String.format("%s,%d,%d,%.4f", datum.pos.getContig(), datum.pos.getStart(), datum.pos.getStop(), datum.lod));
         }
     }
 }
diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java
index ccf4ae17b..b32473b9d 100755
--- a/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java
@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
+import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.datasources.reads.MockLocusShard;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
@@ -78,7 +79,7 @@ public class ReferenceOrderedViewUnitTest extends BaseTest {
     @Test
     public void testSingleBinding() {
         String fileName = testDir + "TabularDataTest.dat";
-        RMDTriplet triplet = new RMDTriplet("tableTest","Table",fileName,RMDStorageType.FILE);
+        RMDTriplet triplet = new RMDTriplet("tableTest","Table",fileName,RMDStorageType.FILE,new Tags());
         ReferenceOrderedDataSource dataSource = new ReferenceOrderedDataSource(triplet,builder,seq.getSequenceDictionary(),genomeLocParser,false);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chrM",1,30)));
@@ -101,10 +102,10 @@ public class ReferenceOrderedViewUnitTest extends BaseTest {
     public void testMultipleBinding() {
         File file = new File(testDir + "TabularDataTest.dat");
 
-        RMDTriplet testTriplet1 = new RMDTriplet("tableTest1","Table",file.getAbsolutePath(),RMDStorageType.FILE);
+        RMDTriplet testTriplet1 = new RMDTriplet("tableTest1","Table",file.getAbsolutePath(),RMDStorageType.FILE,new Tags());
         ReferenceOrderedDataSource dataSource1 = new ReferenceOrderedDataSource(testTriplet1,builder,seq.getSequenceDictionary(),genomeLocParser,false);
 
-        RMDTriplet testTriplet2 = new RMDTriplet("tableTest2","Table",file.getAbsolutePath(),RMDStorageType.FILE);
+        RMDTriplet testTriplet2 = new RMDTriplet("tableTest2","Table",file.getAbsolutePath(),RMDStorageType.FILE,new Tags());
         ReferenceOrderedDataSource dataSource2 = new ReferenceOrderedDataSource(testTriplet2,builder,seq.getSequenceDictionary(),genomeLocParser,false);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chrM",1,30)));
diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java
index 13f0b3ac1..5b0d67e88 100755
--- a/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java
@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.rmd;
 
+import org.broadinstitute.sting.commandline.Tags;
 import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
@@ -73,7 +74,7 @@ public class ReferenceOrderedDataPoolUnitTest extends BaseTest {
         File indexFileName = new File(testDir + "TabularDataTest.dat.idx");
         if (indexFileName.exists()) indexFileName.delete();  
 
-        triplet = new RMDTriplet("tableTest","Table",fileName,RMDStorageType.FILE);
+        triplet = new RMDTriplet("tableTest","Table",fileName,RMDStorageType.FILE,new Tags());
         builder = new RMDTrackBuilder(seq.getSequenceDictionary(),genomeLocParser,null);
     }
 
diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersV2IntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersV2IntegrationTest.java
index 816ba8056..edae5bf9d 100755
--- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersV2IntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersV2IntegrationTest.java
@@ -25,14 +25,14 @@ public class VariantRecalibrationWalkersV2IntegrationTest extends WalkerTest {
     }
 
     VRTest yriTrio = new VRTest("yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf",
-            "aa211561e6e9b1e323dec4eeaa318088",  // tranches
-            "226adf939e90ad20599108e77ad25dae",  // recal file
-            "06c2335e860e19f23bcacff8d4ab906d"); // cut VCF
+            "644e37fe6edaee13ddf9f3c4f0e6f500",  // tranches
+            "e467bfd4ab74c7a7ff303cf810c514b3",  // recal file
+            "05f66c959d1f8e78bcb4298092524921"); // cut VCF
 
     VRTest lowPass = new VRTest("lowpass.N3.chr1.raw.vcf",
-            "f4f2057a8c010206f0f56deff0602452",  // tranches
-            "dd36d252a6dc6e3207addddae731dd88",  // recal file
-            "af4fe8bd0c2eca92d1990b1a49fae810"); // cut VCF
+            "e0a3845619d2138717df39ef1e9ee75f",  // tranches
+            "c3fa524d0bdb40d6bd7aeda9e8dd882c",  // recal file
+            "9f21a668c3fff13f382367851a11303c"); // cut VCF
 
     @DataProvider(name = "VRTest")
     public Object[][] createData1() {
@@ -44,14 +44,14 @@ public class VariantRecalibrationWalkersV2IntegrationTest extends WalkerTest {
         //System.out.printf("PARAMS FOR %s is %s%n", vcf, clusterFile);
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
-                        " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
-                        " -B:hapmap,VCF " + comparisonDataLocation + "Validated/HapMap/3.2/sites_r27_nr.b36_fwd.vcf" +
-                        " -B:omni,VCF " + comparisonDataLocation + "Validated/Omni2.5_chip/1212samples.b36.vcf" +
+                        " -B:dbsnp,DBSNP,known=true,training=false,truth=false,prior=10.0 " + GATKDataLocation + "dbsnp_129_b36.rod" +
+                        " -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 " + comparisonDataLocation + "Validated/HapMap/3.2/sites_r27_nr.b36_fwd.vcf" +
+                        " -B:omni,VCF,known=false,training=true,truth=true,prior=15.0 " + comparisonDataLocation + "Validated/Omni2.5_chip/1212samples.b36.vcf" +
                         " -T ContrastiveRecalibrator" +
                         " -B:input,VCF " + params.inVCF +
                         " -L 1:50,000,000-120,000,000" +
                         " -an QD -an MQ -an SB -an AF" +
-                        " --trustAllPolymorphic" +
+                        " --trustAllPolymorphic" + // for speed
                         " -recalFile %s" +
                         " -tranchesFile %s",
                 Arrays.asList(params.recalMD5, params.tranchesMD5));
diff --git a/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala b/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
index aa044aa28..785e0d42a 100755
--- a/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
+++ b/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
@@ -112,40 +112,40 @@ class MethodsDevelopmentCallingPipeline extends QScript {
               "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.indels.10.mask",
               new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam"),
               new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.vcf"),
-              "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg18.intervals", 2.07, 1.0, !lowPass),
+              "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg18.intervals", 2.07, 99.0, !lowPass),
     "HiSeq19" -> new Target("NA12878.HiSeq19", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37,
               new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.bam"),
               new File("/humgen/gsa-hpprojects/dev/carneiro/hiseq19/analysis/snps/NA12878.HiSeq19.filtered.vcf"),
-              "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 3.0, !lowPass),
+              "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 97.0, !lowPass),
     "GA2hg19" -> new Target("NA12878.GA2.hg19", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37,
               new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.GA2.WGS.bwa.cleaned.hg19.bam"),
               new File("/humgen/gsa-hpprojects/dev/carneiro/hiseq19/analysis/snps/NA12878.GA2.hg19.filtered.vcf"),
-              "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 1.0, !lowPass),
+              "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 99.0, !lowPass),
     "WEx" -> new Target("NA12878.WEx", hg18, dbSNP_hg18_129, hapmap_hg18,
               "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.indels.10.mask",
               new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.WEx.cleaned.recal.bam"),
               new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.vcf"),
-              "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.targets.interval_list", 2.6, 3.0, !lowPass),
+              "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.targets.interval_list", 2.6, 97.0, !lowPass),
     "WExTrio" -> new Target("CEUTrio.WEx", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37,
               new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.bwa.cleaned.recal.bam"),
               new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"),
-              "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, 3.0, !lowPass),
+              "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, 97.0, !lowPass),
     "FIN" -> new Target("FIN", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
               new File("/humgen/1kg/processing/pipeline_test_bams/FIN.79sample.Nov2010.chr20.bam"),
               new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"),         // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
-              "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, 1.0, lowPass),
+              "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, 99.0, lowPass),
     "TGPWExGdA" -> new Target("1000G.WEx.GdA", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
               new File("/humgen/1kg/processing/pipeline_test_bams/Barcoded_1000G_WEx_Reduced_Plate_1.cleaned.list"),        // BUGBUG: reduce from 60 to 20 people
               new File("/humgen/gsa-scr1/delangel/NewUG/calls/AugustRelease.filtered_Q50_QD5.0_SB0.0.allSamples.SNPs_hg19.WEx_UG_newUG_MQC.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
-              "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, 1.0, !lowPass),
+              "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, 99.0, !lowPass),
     "LowPassN60" -> new Target("lowpass.N60", b36, dbSNP_b36, hapmap_b36, indelMask_b36,
               new File("/humgen/1kg/analysis/bamsForDataProcessingPapers/lowpass_b36/lowpass.chr20.cleaned.matefixed.bam"), // the bam list to call from
               new File("/home/radon01/depristo/work/oneOffProjects/VQSRCutByNRS/lowpass.N60.chr20.filtered.vcf"),           // the gold standard VCF file to run through the VQSR
-              "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.b36.intervals", 2.3, 1.0, lowPass),          // chunked interval list to use with Queue's scatter/gather functionality
+              "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.b36.intervals", 2.3, 99.0, lowPass),          // chunked interval list to use with Queue's scatter/gather functionality
     "LowPassEUR363Nov" -> new Target("EUR.nov2010", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
               new File("/humgen/1kg/processing/pipeline_test_bams/EUR.363sample.Nov2010.chr20.bam"),
               new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"),         // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
-              "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, 1.0, lowPass)
+              "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, 99.0, lowPass)
   )
 
 
@@ -189,6 +189,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
 
   // 1.) Unified Genotyper Base
   class GenotyperBase (t: Target) extends UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
+    this.memoryLimit = 3
     this.reference_sequence = t.reference
     this.intervalsString ++= List(t.intervals)
     this.scatterCount = 63 // the smallest interval list has 63 intervals, one for each Mb on chr20
@@ -225,6 +226,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
 
   // 2.) Hard Filtering for indels
   class indelFilter (t: Target) extends VariantFiltration with UNIVERSAL_GATK_ARGS {
+    this.memoryLimit = 2
     this.reference_sequence = t.reference
     this.intervalsString ++= List(t.intervals)
     this.scatterCount = 10
@@ -243,24 +245,24 @@ class MethodsDevelopmentCallingPipeline extends QScript {
 
   // 3.) Variant Quality Score Recalibration - Generate Recalibration table
   class VQSR(t: Target, goldStandard: Boolean) extends ContrastiveRecalibrator with UNIVERSAL_GATK_ARGS {
-    this.memoryLimit = 6
+    this.memoryLimit = 4
     this.reference_sequence = t.reference
     this.intervalsString ++= List(t.intervals)
     this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.rawVCF } )
-    this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile)
+    this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile, "known=false,training=true,truth=true,prior=12.0")
     if( t.hapmapFile.contains("b37") )
-      this.rodBind :+= RodBind("1kg", "VCF", omni_b37)
+      this.rodBind :+= RodBind("omni", "VCF", omni_b37, "known=false,training=true,truth=true,prior=15.0")
     else if( t.hapmapFile.contains("b36") )
-      this.rodBind :+= RodBind("1kg", "VCF", omni_b36)
+      this.rodBind :+= RodBind("omni", "VCF", omni_b36, "known=false,training=true,truth=true,prior=15.0")
     if (t.dbsnpFile.endsWith(".rod"))
-      this.DBSNP = new File(t.dbsnpFile)
+      this.rodBind :+= RodBind("dbsnp", "DBSNP", t.dbsnpFile, "known=true,training=false,truth=false,prior=10.0")
     else if (t.dbsnpFile.endsWith(".vcf"))
-      this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
+      this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile, "known=true,training=false,truth=false,prior=10.0")
     this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
     this.tranches_file = if ( goldStandard ) { t.goldStandardTranchesFile } else { t.tranchesFile }
     this.recal_file = if ( goldStandard ) { t.goldStandardRecalFile } else { t.recalFile }
     this.allPoly = true
-    this.tranche ++= List("0.1", "0.5", "0.7", "1.0", "1.1", "1.2", "1.5", "1.6", "1.7", "1.8", "1.9", "2.0", "2.1", "2.2", "2.5","3.0", "5.0", "10.0")
+    this.tranche ++= List("100.0", "99.9", "99.5", "99.3", "99.0", "98.9", "98.8", "98.5", "98.4", "98.3", "98.2", "98.1", "98.0", "97.9", "97.8", "97.5", "97.0", "95.0", "90.0")
     this.analysisName = t.name + "_VQSR"
     this.jobName =  queueLogDir + t.name + ".VQSR"
   }
@@ -279,9 +281,9 @@ class MethodsDevelopmentCallingPipeline extends QScript {
     this.jobName =  queueLogDir + t.name + ".applyVQSR"
   }
 
-
-  // 6.) Variant Evaluation Base(OPTIONAL)
+  // 5.) Variant Evaluation Base(OPTIONAL)
   class EvalBase(t: Target) extends VariantEval with UNIVERSAL_GATK_ARGS {
+    this.memoryLimit = 3
     this.reference_sequence = t.reference
     this.rodBind :+= RodBind("comphapmap", "VCF", t.hapmapFile)
     this.intervalsString ++= List(t.intervals)
@@ -292,7 +294,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
     this.sample = samples
   }
 
-  // 6a.) SNP Evaluation (OPTIONAL) based on the cut vcf
+  // 5a.) SNP Evaluation (OPTIONAL) based on the cut vcf
   class snpEvaluation(t: Target) extends EvalBase(t) {
     if (t.reference == b37 || t.reference == hg19) this.rodBind :+= RodBind("compomni", "VCF", omni_b37)
     this.rodBind :+= RodBind("eval", "VCF", t.recalibratedVCF )
@@ -301,7 +303,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
     this.jobName =  queueLogDir + t.name + ".snp.eval"
   }
 
-  // 6b.) Indel Evaluation (OPTIONAL)
+  // 5b.) Indel Evaluation (OPTIONAL)
   class indelEvaluation(t: Target) extends EvalBase(t) {
     this.rodBind :+= RodBind("eval", "VCF", t.filteredIndelVCF)
     this.evalModule :+= "IndelStatistics"