diff --git a/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java b/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java
index 8ad92e2d1..ec2117127 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java
@@ -26,13 +26,13 @@ package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
-import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 
-import java.util.*;
+import java.util.List;
 
 /**
+ * A RodBinding representing a walker argument that gets bound to a ROD track.
  *
+ * There is no constraint on the type of the ROD bound.
  */
 public class RodBinding {
     final String variableName;
@@ -53,23 +53,23 @@ public class RodBinding {
         return source;
     }
 
-    public List<Object> getValues(RefMetaDataTracker tracker) {
+    public List<Object> getValues(final RefMetaDataTracker tracker) {
         return tracker.getValues(variableName);
     }
 
-    public <T> List<T> getValues(RefMetaDataTracker tracker, Class<T> clazz) {
+    public <T> List<T> getValues(final RefMetaDataTracker tracker, final Class<T> clazz) {
         return tracker.getValues(variableName, clazz);
     }
 
-    public <T> T getFirstValue(RefMetaDataTracker tracker, Class<T> clazz) {
+    public <T> T getFirstValue(final RefMetaDataTracker tracker, final Class<T> clazz) {
         return tracker.getFirstValue(variableName, clazz);
     }
 
-    public boolean hasValues(RefMetaDataTracker tracker) {
+    public boolean hasValues(final RefMetaDataTracker tracker) {
         return tracker.hasValues(variableName);
     }
 
-    public List<GATKFeature> getValuesAsGATKFeatures(RefMetaDataTracker tracker) {
+    public List<GATKFeature> getValuesAsGATKFeatures(final RefMetaDataTracker tracker) {
         return tracker.getValuesAsGATKFeatures(variableName);
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/commandline/VariantContextRodBinding.java b/public/java/src/org/broadinstitute/sting/commandline/VariantContextRodBinding.java
index a9ce824f8..f5e29986e 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/VariantContextRodBinding.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/VariantContextRodBinding.java
@@ -29,42 +29,54 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.io.File;
-import java.util.List;
+import java.util.Collection;
 
 /**
- *
+ * A RodBinding representing a walker argument that gets bound to a ROD track containing VariantContexts
  */
 public class VariantContextRodBinding extends RodBinding {
+    /**
+     * Create a new RodBinding specialized to provide VariantContexts.
+     * @param variableName the name of the field in the walker that we will bind the ROD track too
+     * @param sourceFile the data source from which we will read the VCs
+     * @param parser the Engine parser used to obtain information about this argument, such as its underlying file type
+     */
     protected VariantContextRodBinding(final String variableName, final String sourceFile, final ParsingEngine parser) {
         super(variableName, sourceFile, parser);
     }
 
-    public VariantContext getVariantContext(RefMetaDataTracker tracker, ReferenceContext ref, GenomeLoc loc) {
-        return tracker.getVariantContext(ref, variableName, loc);
+    /**
+     * Forwarding method to identical tracker method
+     */
+    public Collection<VariantContext> getVariantContexts(final RefMetaDataTracker tracker,
+                                                         final ReferenceContext ref,
+                                                         final GenomeLoc curLocation,
+                                                         final boolean requireStartHere,
+                                                         final boolean takeFirstOnly ) {
+        return tracker.getVariantContexts(ref, variableName, curLocation, requireStartHere, takeFirstOnly);
     }
 
-//    public Collection<VariantContext> getAllVariantContexts(ReferenceContext ref) {
-//    }
-//
-//    public Collection<VariantContext> getAllVariantContexts(ReferenceContext ref, GenomeLoc curLocation) {
-//    }
-//
-//    public Collection<VariantContext> getAllVariantContexts(ReferenceContext ref, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
-//    }
-//
-//    public Collection<VariantContext> getVariantContexts(ReferenceContext ref, String name, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
-//    }
-//
-//    public Collection<VariantContext> getVariantContexts(ReferenceContext ref, Collection<String> names, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
-//    }
-//
-//    public Collection<VariantContext> getVariantContextsByPrefix(ReferenceContext ref, Collection<String> names, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
-//    }
-//
-//    public VariantContext getVariantContext(ReferenceContext ref, String name, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere ) {
-//    }
-//
-//    public VariantContext getVariantContext(ReferenceContext ref, String name, GenomeLoc curLocation) {
-//    }
+    /**
+     * Forwarding method to identical tracker method
+     * @param tracker
+     * @param ref
+     * @param curLocation
+     * @param requireStartHere
+     * @return
+     */
+    public VariantContext getVariantContext(final RefMetaDataTracker tracker,
+                                            final ReferenceContext ref,
+                                            final GenomeLoc curLocation,
+                                            final boolean requireStartHere ) {
+        return tracker.getVariantContext(ref, variableName, curLocation, requireStartHere);
+    }
+
+    /**
+     * Forwarding method to identical tracker method
+     */
+    public VariantContext getVariantContext(final RefMetaDataTracker tracker,
+                                            final ReferenceContext ref,
+                                            final GenomeLoc curLocation) {
+        return tracker.getVariantContext(ref, variableName, curLocation);
+    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
index 926158a36..40cf4cbd4 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
@@ -54,7 +54,7 @@ public class RefMetaDataTracker {
      *
      * Important: The list returned by this function is guaranteed not to be null, but may be empty!
      */
-    public <T> List<T> getValues(final String name, Class<T> clazz) {
+    public <T> List<T> getValues(final String name, final Class<T> clazz) {
         RODRecordList list = getTrackDataByName(name);
 
         if (list == null)
@@ -73,10 +73,10 @@ public class RefMetaDataTracker {
     }
 
     /**
-     * get a singleton record, given the name and a type.  This function will return the first record at the current position seen,
-     * and emit a logger warning if there were more than one option.
+     * get a singleton record, given the name and a type.  This function will return the first record at the
+     * current position seen.  The object is cast into a type clazz, or thoses an error if this isn't possible.
      *
-     * WARNING: we now suppport more than one RMD at a single position for all tracks.  If there are
+     * * WARNING: we now suppport more than one RMD at a single position for all tracks.  If there are
      * are multiple RMD objects at this location, there is no contract for which object this method will pick, and which object gets
      * picked may change from time to time!  BE WARNED!
      * 
@@ -85,7 +85,7 @@ public class RefMetaDataTracker {
      * @param <T> the type to parameterize on, matching the clazz argument
      * @return a record of type T, or null if no record is present.
      */
-    public <T> T getFirstValue(final String name, Class<T> clazz) {
+    public <T> T getFirstValue(final String name, final Class<T> clazz) {
         RODRecordList objects = getTrackDataByName(name);
 
         // if empty or null return null;
@@ -172,6 +172,8 @@ public class RefMetaDataTracker {
      * Binds the list of reference ordered data records (RMDs) to track name at this site.  Should be used only by the traversal
      * system to provide access to RMDs in a structured way to the walkers.
      *
+     * DO NOT USE THIS FUNCTION UNLESS YOU ARE THE GATK ENGINE
+     *
      * @param name the name of the track
      * @param rod the collection of RMD data
      */
@@ -180,6 +182,13 @@ public class RefMetaDataTracker {
         map.put(canonicalName(name), rod);
     }
 
+    // ------------------------------------------------------------------------------------------
+    //
+    //
+    // VariantContext helpers
+    //
+    //
+    // ------------------------------------------------------------------------------------------
 
     /**
      * Converts all possible ROD tracks to VariantContexts objects, of all types, allowing any start and any number
@@ -189,8 +198,8 @@ public class RefMetaDataTracker {
      * @param ref                reference context
      * @return variant context
      */
-    public Collection<VariantContext> getAllVariantContexts(ReferenceContext ref) {
-        return getAllVariantContexts(ref, null, null, false, false);
+    public Collection<VariantContext> getAllVariantContexts(final ReferenceContext ref) {
+        return getAllVariantContexts(ref, null, false, false);
     }
 
     /**
@@ -199,8 +208,9 @@ public class RefMetaDataTracker {
      * @param curLocation
      * @return
      */
-    public Collection<VariantContext> getAllVariantContexts(ReferenceContext ref, GenomeLoc curLocation) {
-        return getAllVariantContexts(ref, null, curLocation, true, false);
+    public Collection<VariantContext> getAllVariantContexts(final ReferenceContext ref,
+                                                            final GenomeLoc curLocation) {
+        return getAllVariantContexts(ref, curLocation, true, false);
     }
 
     /**
@@ -215,17 +225,19 @@ public class RefMetaDataTracker {
      * The name of each VariantContext corresponds to the ROD name.
      *
      * @param ref                reference context
-     * @param allowedTypes       allowed types
      * @param curLocation        location
      * @param requireStartHere   do we require the rod to start at this location?
      * @param takeFirstOnly      do we take the first rod only?
      * @return variant context
      */
-    public Collection<VariantContext> getAllVariantContexts(ReferenceContext ref, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
+    public Collection<VariantContext> getAllVariantContexts(final ReferenceContext ref,
+                                                            final GenomeLoc curLocation,
+                                                            final boolean requireStartHere,
+                                                            final boolean takeFirstOnly ) {
         List<VariantContext> contexts = new ArrayList<VariantContext>();
 
         for ( RODRecordList rodList : getBoundRodTracks() ) {
-            addVariantContexts(contexts, rodList, ref, allowedTypes, curLocation, requireStartHere, takeFirstOnly);
+            addVariantContexts(contexts, rodList, ref, curLocation, requireStartHere, takeFirstOnly);
         }
 
         return contexts;
@@ -239,31 +251,30 @@ public class RefMetaDataTracker {
      * @param ref                ReferenceContext to enable conversion to variant context
      * @param name               name
      * @param curLocation        location
-     * @param allowedTypes       allowed types
      * @param requireStartHere   do we require the rod to start at this location?
      * @param takeFirstOnly      do we take the first rod only?
      * @return variant context
      */
-//    public Collection<VariantContext> getVariantContexts(String name, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
-//        return getVariantContexts(null, Arrays.asList(name), allowedTypes, curLocation, requireStartHere, takeFirstOnly);
-//    }
-
-    public Collection<VariantContext> getVariantContexts(ReferenceContext ref, String name, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
-        return getVariantContexts(ref, Arrays.asList(name), allowedTypes, curLocation, requireStartHere, takeFirstOnly);
+    public Collection<VariantContext> getVariantContexts(final ReferenceContext ref,
+                                                         final String name,
+                                                         final GenomeLoc curLocation,
+                                                         final boolean requireStartHere,
+                                                         final boolean takeFirstOnly ) {
+        return getVariantContexts(ref, Arrays.asList(name), curLocation, requireStartHere, takeFirstOnly);
     }
 
-//    public Collection<VariantContext> getVariantContexts(Collection<String> names, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
-//        return getVariantContexts(null, names, allowedTypes, curLocation, requireStartHere, takeFirstOnly);
-//    }
-
-    public Collection<VariantContext> getVariantContexts(ReferenceContext ref, Collection<String> names, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
+    public Collection<VariantContext> getVariantContexts(final ReferenceContext ref,
+                                                         final Collection<String> names,
+                                                         final GenomeLoc curLocation,
+                                                         final boolean requireStartHere,
+                                                         final boolean takeFirstOnly ) {
         Collection<VariantContext> contexts = new ArrayList<VariantContext>();
 
         for ( String name : names ) {
             RODRecordList rodList = getTrackDataByName(name); // require that the name is an exact match
 
             if ( rodList != null )
-                addVariantContexts(contexts, rodList, ref, allowedTypes, curLocation, requireStartHere, takeFirstOnly );
+                addVariantContexts(contexts, rodList, ref, curLocation, requireStartHere, takeFirstOnly );
         }
 
         return contexts;
@@ -275,12 +286,14 @@ public class RefMetaDataTracker {
      *
      * @param name               name
      * @param curLocation        location
-     * @param allowedTypes       allowed types
      * @param requireStartHere   do we require the rod to start at this location?
      * @return variant context
      */
-    public VariantContext getVariantContext(ReferenceContext ref, String name, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere ) {
-        Collection<VariantContext> contexts = getVariantContexts(ref, name, allowedTypes, curLocation, requireStartHere, false );
+    public VariantContext getVariantContext(final ReferenceContext ref,
+                                            final String name,
+                                            final GenomeLoc curLocation,
+                                            final boolean requireStartHere ) {
+        Collection<VariantContext> contexts = getVariantContexts(ref, name, curLocation, requireStartHere, false );
 
         if ( contexts.size() > 1 )
             throw new ReviewedStingException("Requested a single VariantContext object for track " + name + " but multiple variants were present at position " + curLocation);
@@ -299,24 +312,27 @@ public class RefMetaDataTracker {
      * @param curLocation
      * @return
      */
-    public VariantContext getVariantContext(ReferenceContext ref, String name, GenomeLoc curLocation) {
-        return getVariantContext(ref, name, null, curLocation, true);
+    public VariantContext getVariantContext(final ReferenceContext ref,
+                                            final String name,
+                                            final GenomeLoc curLocation) {
+        return getVariantContext(ref, name, curLocation, true);
     }
 
-    private void addVariantContexts(Collection<VariantContext> contexts, RODRecordList rodList, ReferenceContext ref, EnumSet<VariantContext.Type> allowedTypes, GenomeLoc curLocation, boolean requireStartHere, boolean takeFirstOnly ) {
+    private void addVariantContexts(final Collection<VariantContext> contexts,
+                                    final RODRecordList rodList,
+                                    final ReferenceContext ref,
+                                    final GenomeLoc curLocation,
+                                    final boolean requireStartHere,
+                                    final boolean takeFirstOnly ) {
         for ( GATKFeature rec : rodList ) {
             if ( VariantContextAdaptors.canBeConvertedToVariantContext(rec.getUnderlyingObject()) ) {
                 // ok, we might actually be able to turn this record in a variant context
-                VariantContext vc = VariantContextAdaptors.toVariantContext(rodList.getName(), rec.getUnderlyingObject(), ref);
+                final VariantContext vc = VariantContextAdaptors.toVariantContext(rodList.getName(), rec.getUnderlyingObject(), ref);
 
                 if ( vc == null ) // sometimes the track has odd stuff in it that can't be converted
                     continue;
 
-                // now, let's decide if we want to keep it
-                boolean goodType = allowedTypes == null || allowedTypes.contains(vc.getType());
-                boolean goodPos = ! requireStartHere || rec.getLocation().getStart() == curLocation.getStart();
-
-                if ( goodType && goodPos ) {  // ok, we are going to keep this thing
+                if ( ! requireStartHere || rec.getLocation().getStart() == curLocation.getStart() ) {  // ok, we are going to keep this thing
                     contexts.add(vc);
 
                     if ( takeFirstOnly )
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
index acbeee3b2..207c4118d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -202,7 +202,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", null, context.getLocation(), true, false);
+        Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", context.getLocation(), true, false);
         if ( VCs.size() == 0 )
             return 0;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
index 3cf96d443..73249d343 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
@@ -203,7 +203,7 @@ public class VariantAnnotatorEngine {
                     infoAnnotations.put(VariantContext.ID_KEY, rsID);
             } else {
                 boolean overlapsComp = false;
-                for ( VariantContext comp : tracker.getVariantContexts(ref, dbSet.getKey(), null, ref.getLocus(), false, false) ) {
+                for ( VariantContext comp : tracker.getVariantContexts(ref, dbSet.getKey(), ref.getLocus(), false, false) ) {
                     if ( !comp.isFiltered() ) {
                         overlapsComp = true;
                         break;
@@ -216,7 +216,7 @@ public class VariantAnnotatorEngine {
 
     private void annotateExpressions(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, Object> infoAnnotations) {
         for ( VAExpression expression : requestedExpressions ) {
-            Collection<VariantContext> VCs = tracker.getVariantContexts(ref, expression.bindingName, null, ref.getLocus(), false, true);
+            Collection<VariantContext> VCs = tracker.getVariantContexts(ref, expression.bindingName, ref.getLocus(), false, true);
             if ( VCs.size() == 0 )
                 continue;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java
index b42310780..82d2af283 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java
@@ -244,7 +244,7 @@ public class GenomicAnnotator extends RodWalker<Integer, Integer> implements Tre
             return 0;
 
         Set<VariantContext> results = new LinkedHashSet<VariantContext>();
-        for (VariantContext vc : tracker.getVariantContexts(ref, "variant", null, context.getLocation(), true, false)) {
+        for (VariantContext vc : tracker.getVariantContexts(ref, "variant", context.getLocation(), true, false)) {
             if ( (vc.isFiltered() && IGNORE_FILTERED_SITES) ||
                     (vc.isVariant() && !vc.isBiallelic()) ) {
                 results.add(vc);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
index 0720e5a16..5499c99b0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
@@ -119,9 +119,9 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
             return 0;
 
         GenomeLoc loc = context.getLocation();
-        VariantContext vc_input = tracker.getVariantContext(ref,INPUT_ROD_NAME, null, loc, true);
+        VariantContext vc_input = tracker.getVariantContext(ref,INPUT_ROD_NAME, loc, true);
 
-        VariantContext vc_comp = tracker.getVariantContext(ref,COMP_ROD_NAME, null, loc, true);
+        VariantContext vc_comp = tracker.getVariantContext(ref,COMP_ROD_NAME, loc, true);
 
         if ( vc_input == null  )
             return 0;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
index 3eed12992..b20b44cd6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
@@ -121,8 +121,8 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
     public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
         if( tracker != null ) {
             GenomeLoc loc = context.getLocation();
-            VariantContext variant_eval = tracker.getVariantContext(ref, ROD_NAME, null, loc, true);
-            VariantContext validation_eval = tracker.getVariantContext(ref,VALIDATION_ROD_NAME,null,loc, true);
+            VariantContext variant_eval = tracker.getVariantContext(ref, ROD_NAME, loc, true);
+            VariantContext validation_eval = tracker.getVariantContext(ref,VALIDATION_ROD_NAME, loc, true);
 
             if ( goodSite(variant_eval,validation_eval) ) {
                 if ( useValidation(validation_eval, ref) ) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java
index f6cd1d636..41b35321e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java
@@ -102,7 +102,7 @@ public class VariantsToBeagleUnphasedWalker extends RodWalker<Integer, Integer>
     public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
         if( tracker != null ) {
             GenomeLoc loc = context.getLocation();
-            VariantContext vc = tracker.getVariantContext(ref, ROD_NAME, null, loc, true);
+            VariantContext vc = tracker.getVariantContext(ref, ROD_NAME, loc, true);
 
             if ( ProduceBeagleInputWalker.canBeOutputToBeagle(vc) ) {
                 // do we want to hold back this site?
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
index eb62190fb..2e96fc172 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
@@ -149,7 +149,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> VCs = tracker.getVariantContexts(ref, INPUT_VARIANT_ROD_BINDING_NAME, null, context.getLocation(), true, false);
+        Collection<VariantContext> VCs = tracker.getVariantContexts(ref, INPUT_VARIANT_ROD_BINDING_NAME, context.getLocation(), true, false);
 
         // is there a SNP mask present?
         boolean hasMask = tracker.getValues("mask").size() > 0;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index 60ea601d5..c76fea34f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -293,6 +293,9 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
         return aList;
 
     }
+
+    private final static EnumSet<VariantContext.Type> allowableTypes = EnumSet.of(VariantContext.Type.INDEL, VariantContext.Type.MIXED);
+
     public Allele getLikelihoods(RefMetaDataTracker tracker,
                                  ReferenceContext ref,
                                  Map<String, AlignmentContext> contexts,
@@ -318,11 +321,10 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
             haplotypeMap.clear();
 
             if (getAlleleListFromVCF) {
-                 EnumSet<VariantContext.Type> allowableTypes = EnumSet.of(VariantContext.Type.INDEL);
-                 allowableTypes.add(VariantContext.Type.MIXED);
-                 for( final VariantContext vc_input : tracker.getVariantContexts(ref, "alleles",
-                         allowableTypes, ref.getLocus(), false, false) ) {
-                      if( vc_input != null && ref.getLocus().getStart() == vc_input.getStart()) {
+                 for( final VariantContext vc_input : tracker.getVariantContexts(ref, "alleles", ref.getLocus(), false, false) ) {
+                      if( vc_input != null &&
+                              allowableTypes.contains(vc_input.getType()) &&
+                              ref.getLocus().getStart() == vc_input.getStart()) {
                          vc = vc_input;
                          break;
                      }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
index 3e3cd128b..30a86249d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
@@ -63,7 +63,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
         VariantContext vc = null;
 
         // search for usable record
-        for( final VariantContext vc_input : tracker.getVariantContexts(ref, "alleles", null, ref.getLocus(), true, false) ) {
+        for( final VariantContext vc_input : tracker.getVariantContexts(ref, "alleles", ref.getLocus(), true, false) ) {
             if ( vc_input != null && ! vc_input.isFiltered() && (! requireSNP || vc_input.isSNP() )) {
                 if ( vc == null ) {
                     vc = vc_input;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java
index 68d8f9b54..6e03088e7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java
@@ -96,7 +96,7 @@ public class UGCallVariants extends RodWalker<VariantCallContext, Integer> {
 
         List<VariantContext> VCs = new ArrayList<VariantContext>();
         for ( String name : trackNames ) {
-            Collection<VariantContext> vc = tracker.getVariantContexts(ref, name, null, context.getLocation(), true, true);
+            Collection<VariantContext> vc = tracker.getVariantContexts(ref, name, context.getLocation(), true, true);
             VCs.addAll(vc);
         }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
index 22672b7a9..263dffb6c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
@@ -155,7 +155,7 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
 
         boolean requireStartHere = false; // see EVERY site of the MNP
         boolean takeFirstOnly = false; // take as many entries as the VCF file has
-        for (VariantContext vc : tracker.getVariantContexts(ref, rodNames, null, context.getLocation(), requireStartHere, takeFirstOnly)) {
+        for (VariantContext vc : tracker.getVariantContexts(ref, rodNames, context.getLocation(), requireStartHere, takeFirstOnly)) {
             GenomeLoc vcLoc = VariantContextUtils.getLocation(locParser, vc);
             boolean atStartOfVc = curLocus.getStart() == vcLoc.getStart();
             boolean atEndOfVc = curLocus.getStart() == vcLoc.getStop();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java
index 298d8d6c8..a4b49b8ff 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java
@@ -44,8 +44,8 @@ public class MergeAndMatchHaplotypes extends RodWalker<Integer, Integer> {
     @Override
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         if (tracker != null) {
-            Collection<VariantContext> pbts = tracker.getVariantContexts(ref, "pbt", null, ref.getLocus(), true, true);
-            Collection<VariantContext> rbps = tracker.getVariantContexts(ref, "rbp", null, ref.getLocus(), true, true);
+            Collection<VariantContext> pbts = tracker.getVariantContexts(ref, "pbt", ref.getLocus(), true, true);
+            Collection<VariantContext> rbps = tracker.getVariantContexts(ref, "rbp", ref.getLocus(), true, true);
 
             VariantContext pbt = pbts.iterator().hasNext() ? pbts.iterator().next() : null;
             VariantContext rbp = rbps.iterator().hasNext() ? rbps.iterator().next() : null;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java
index 5bd438605..d36da9835 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java
@@ -103,7 +103,7 @@ public class MergeMNPsWalker extends RodWalker<Integer, Integer> {
 
         boolean requireStartHere = true; // only see each VariantContext once
         boolean takeFirstOnly = false; // take as many entries as the VCF file has
-        for (VariantContext vc : tracker.getVariantContexts(ref, rodNames, null, context.getLocation(), requireStartHere, takeFirstOnly))
+        for (VariantContext vc : tracker.getVariantContexts(ref, rodNames, context.getLocation(), requireStartHere, takeFirstOnly))
             writeVCF(vc);
 
         return 0;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
index be15d4541..73d7fa529 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
@@ -140,7 +140,7 @@ public class MergeSegregatingAlternateAllelesWalker extends RodWalker<Integer, I
 
         boolean requireStartHere = true; // only see each VariantContext once
         boolean takeFirstOnly = false; // take as many entries as the VCF file has
-        for (VariantContext vc : tracker.getVariantContexts(ref, rodNames, null, context.getLocation(), requireStartHere, takeFirstOnly))
+        for (VariantContext vc : tracker.getVariantContexts(ref, rodNames, context.getLocation(), requireStartHere, takeFirstOnly))
             writeVCF(vc);
 
         return 0;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
index cf4afbb6d..5daaf257a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
@@ -289,7 +289,7 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
     @Override
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         if (tracker != null) {
-            Collection<VariantContext> vcs = tracker.getVariantContexts(ref, ROD_NAME, null, context.getLocation(), true, true);
+            Collection<VariantContext> vcs = tracker.getVariantContexts(ref, ROD_NAME, context.getLocation(), true, true);
 
             for (VariantContext vc : vcs) {
                 Map<String, Genotype> genotypeMap = vc.getGenotypes();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index 9702fd18c..f96cec1b7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -209,7 +209,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
 
         boolean requireStartHere = true; // only see each VariantContext once
         boolean takeFirstOnly = false; // take as many entries as the VCF file has
-        for (VariantContext vc : tracker.getVariantContexts(ref, rodNames, null, context.getLocation(), requireStartHere, takeFirstOnly)) {
+        for (VariantContext vc : tracker.getVariantContexts(ref, rodNames, context.getLocation(), requireStartHere, takeFirstOnly)) {
             if (samplesToPhase != null) vc = reduceVCToSamples(vc, samplesToPhase);
 
             if (ReadBackedPhasingWalker.processVariantInPhasing(vc)) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
index 1b302425d..c1611649f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
@@ -40,9 +40,12 @@ public class Novelty extends VariantStratifier implements StandardStratification
                         allowableTypes.add(eval.getType());
                     }
 
-                    Collection<VariantContext> knownComps = tracker.getVariantContexts(ref, knownName, allowableTypes, ref.getLocus(), true, true);
-
-                    isNovel = knownComps.size() == 0;
+                    Collection<VariantContext> knownComps = tracker.getVariantContexts(ref, knownName, ref.getLocus(), true, true);
+                    for ( VariantContext c : knownComps )
+                        if ( allowableTypes.contains(c.getType()) ) {
+                            isNovel = false;
+                            break;
+                        }
 
                     break;
                 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
index 0a915db37..7beb94593 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
@@ -270,30 +270,7 @@ public class VariantEvalUtils {
                                                                    Set<String> compNames,
                                                                    Set<String> evalNames,
                                                                    boolean dynamicSelectTypes ) {
-        if ( dynamicSelectTypes ) { // todo -- this code is really conceptually broken
-            EnumSet<VariantContext.Type> allowableTypes = EnumSet.of(VariantContext.Type.NO_VARIATION);
-
-            if (tracker != null) {
-                Collection<VariantContext> evalvcs = tracker.getVariantContexts(ref, evalNames, null, ref.getLocus(), true, false);
-
-                for (VariantContext vc : evalvcs) {
-                    allowableTypes.add(vc.getType());
-                }
-
-                if (allowableTypes.size() == 1) {
-                    // We didn't find any variation in the eval track, so now let's look at the comp track for allowable types
-                    Collection<VariantContext> compvcs = tracker.getVariantContexts(ref, compNames, null, ref.getLocus(), true, false);
-
-                    for (VariantContext vc : compvcs) {
-                        allowableTypes.add(vc.getType());
-                    }
-                }
-            }
-
-            return allowableTypes;
-        } else {
-            return EnumSet.allOf(VariantContext.Type.class);
-        }
+        return EnumSet.allOf(VariantContext.Type.class);
     }
 
     /**
@@ -359,7 +336,7 @@ public class VariantEvalUtils {
         for (String trackName : trackNames) {
             HashMap<String, VariantContext> vcs = new HashMap<String, VariantContext>();
 
-            Collection<VariantContext> contexts = tracker == null ? null : tracker.getVariantContexts(ref, trackName, allowableTypes, ref.getLocus(), true, true);
+            Collection<VariantContext> contexts = tracker == null ? null : tracker.getVariantContexts(ref, trackName, ref.getLocus(), true, true);
             VariantContext vc = contexts != null && contexts.size() == 1 ? contexts.iterator().next() : null;
 
             // First, filter the VariantContext to represent only the samples for evaluation
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
index b195fd35f..5fb738944 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
@@ -168,7 +168,7 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
             return 1;
         }
 
-        for( VariantContext vc : tracker.getVariantContexts(ref, inputNames, null, context.getLocation(), true, false) ) {
+        for( VariantContext vc : tracker.getVariantContexts(ref, inputNames, context.getLocation(), true, false) ) {
             if( vc != null ) {
                 if( VariantRecalibrator.checkRecalibrationMode( vc, MODE ) && (vc.isNotFiltered() || ignoreInputFilterSet.containsAll(vc.getFilters())) ) {
                     String filterString = null;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index 67d54a408..c76efc2dd 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -258,7 +258,7 @@ public class VariantDataManager {
         datum.consensusCount = 0;
 
         for( final TrainingSet trainingSet : trainingSets ) {
-            for( final VariantContext trainVC : tracker.getVariantContexts( ref, trainingSet.name, null, context.getLocation(), false, false ) ) {
+            for( final VariantContext trainVC : tracker.getVariantContexts( ref, trainingSet.name, context.getLocation(), false, false ) ) {
                 if( trainVC != null && trainVC.isNotFiltered() && trainVC.isVariant() &&
                         ((evalVC.isSNP() && trainVC.isSNP()) || ((evalVC.isIndel()||evalVC.isMixed()) && (trainVC.isIndel()||trainVC.isMixed()))) &&
                         (TRUST_ALL_POLYMORPHIC || !trainVC.hasGenotypes() || trainVC.isPolymorphic()) ) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 76c888640..7e1d931c9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -163,7 +163,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
             return mapList;
         }
 
-        for( final VariantContext vc : tracker.getVariantContexts(ref, inputNames, null, context.getLocation(), true, false) ) {
+        for( final VariantContext vc : tracker.getVariantContexts(ref, inputNames, context.getLocation(), true, false) ) {
             if( vc != null && ( vc.isNotFiltered() || ignoreInputFilterSet.containsAll(vc.getFilters()) ) ) {
                 if( checkRecalibrationMode( vc, VRAC.MODE ) ) {
                     final VariantDatum datum = new VariantDatum();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index 9c2a520ef..2083802d1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -150,7 +150,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
 
         // get all of the vcf rods at this locus
         // Need to provide reference bases to simpleMerge starting at current locus
-        Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, null, context.getLocation(), true, false);
+        Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, context.getLocation(), true, false);
 
         if ( sitesOnlyVCF ) {
             vcs = VariantContextUtils.sitesOnlyVariantContexts(vcs);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
index b45ee1b67..97cb9a6e3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
@@ -85,7 +85,7 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", null, context.getLocation(), true, false);
+        Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", context.getLocation(), true, false);
         for ( VariantContext vc : VCs )
             filterAndWrite(ref.getBases(), vc);
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
index 2ebd183f4..566333d3f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
@@ -68,7 +68,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", null, context.getLocation(), true, false);
+        Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", context.getLocation(), true, false);
 
         int changedSites = 0;
         for ( VariantContext vc : VCs )
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
index 4f05c8aac..061c3b256 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
@@ -143,7 +143,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", null, context.getLocation(), true, false);
+        Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", context.getLocation(), true, false);
         for ( VariantContext vc : VCs )
             convertAndWrite(vc, ref);
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
index f0756d884..99e12c836 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
@@ -97,7 +97,7 @@ public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> vcs = tracker.getVariantContexts(ref, INPUT_VARIANT_ROD_BINDING_NAME, null, context.getLocation(), true, false);
+        Collection<VariantContext> vcs = tracker.getVariantContexts(ref, INPUT_VARIANT_ROD_BINDING_NAME, context.getLocation(), true, false);
         for ( VariantContext vc : vcs ) {
             int random = GenomeAnalysisEngine.getRandomGenerator().nextInt(1000);
             if ( random < iFraction )
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index e1a3659b8..0efed393a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -317,7 +317,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> vcs = tracker.getVariantContexts(ref, variantRodName, null, context.getLocation(), true, false);
+        Collection<VariantContext> vcs = tracker.getVariantContexts(ref, variantRodName, context.getLocation(), true, false);
 
         if ( vcs == null || vcs.size() == 0) {
             return 0;
@@ -345,12 +345,12 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
                     break;
             }
             if (DISCORDANCE_ONLY) {
-                Collection<VariantContext> compVCs = tracker.getVariantContexts(ref, discordanceRodName, null, context.getLocation(), true, false);
+                Collection<VariantContext> compVCs = tracker.getVariantContexts(ref, discordanceRodName, context.getLocation(), true, false);
                 if (!isDiscordant(vc, compVCs))
                     return 0;
             }
             if (CONCORDANCE_ONLY) {
-                Collection<VariantContext> compVCs = tracker.getVariantContexts(ref, concordanceRodName, null, context.getLocation(), true, false);
+                Collection<VariantContext> compVCs = tracker.getVariantContexts(ref, concordanceRodName, context.getLocation(), true, false);
                 if (!isConcordant(vc, compVCs))
                     return 0;
             }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
index 5e779097a..756a00731 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
@@ -86,7 +86,7 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", null, context.getLocation(), true, false);
+        Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", context.getLocation(), true, false);
         for ( VariantContext vc : VCs )
             validate(vc, tracker, ref);
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
index 4f5a5652f..8f0fdd907 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
@@ -90,21 +90,23 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
         Collection<VariantContext> contexts = getVariantContexts(tracker, ref);
 
         for ( VariantContext vc : contexts ) {
-            Map<String, Object> attrs = new HashMap<String, Object>(vc.getAttributes());
-            if ( rsID != null && !vc.hasID() ) {
-                attrs.put(VariantContext.ID_KEY, rsID);
-                vc = VariantContext.modifyAttributes(vc, attrs);
-            }
+            if ( ALLOWED_VARIANT_CONTEXT_TYPES.contains(vc.getType()) ) {
+                Map<String, Object> attrs = new HashMap<String, Object>(vc.getAttributes());
+                if ( rsID != null && !vc.hasID() ) {
+                    attrs.put(VariantContext.ID_KEY, rsID);
+                    vc = VariantContext.modifyAttributes(vc, attrs);
+                }
 
-            // set the appropriate sample name if necessary
-            if ( sampleName != null && vc.hasGenotypes() && vc.hasGenotype(INPUT_ROD_NAME) ) {
-                Genotype g = Genotype.modifyName(vc.getGenotype(INPUT_ROD_NAME), sampleName);
-                Map<String, Genotype> genotypes = new HashMap<String, Genotype>();
-                genotypes.put(sampleName, g);
-                vc = VariantContext.modifyGenotypes(vc, genotypes);
-            }
+                // set the appropriate sample name if necessary
+                if ( sampleName != null && vc.hasGenotypes() && vc.hasGenotype(INPUT_ROD_NAME) ) {
+                    Genotype g = Genotype.modifyName(vc.getGenotype(INPUT_ROD_NAME), sampleName);
+                    Map<String, Genotype> genotypes = new HashMap<String, Genotype>();
+                    genotypes.put(sampleName, g);
+                    vc = VariantContext.modifyGenotypes(vc, genotypes);
+                }
 
-            writeRecord(vc, tracker, ref.getBase());
+                writeRecord(vc, tracker, ref.getBase());
+            }
         }
 
         return 1;
@@ -160,7 +162,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
         }
 
         // for everything else, we can just convert to VariantContext
-        return tracker.getVariantContexts(ref, INPUT_ROD_NAME, ALLOWED_VARIANT_CONTEXT_TYPES, ref.getLocus(), true, false);
+        return tracker.getVariantContexts(ref, INPUT_ROD_NAME, ref.getLocus(), true, false);
     }
 
     private DbSNPFeature getDbsnpFeature(String rsID) {