diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
index 914f54363..b4739f366 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
@@ -25,15 +25,10 @@
 
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
-import org.broad.tribble.bed.BEDCodec;
-import org.broad.tribble.dbsnp.DbSNPCodec;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.ArgumentCollection;
-import org.broadinstitute.sting.commandline.Gather;
-import org.broadinstitute.sting.commandline.Output;
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter;
 import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -42,8 +37,6 @@ import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broadinstitute.sting.utils.collections.NestedHashMap;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -94,13 +87,18 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
     /////////////////////////////
     @ArgumentCollection private RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
 
-    @Output
-    PrintStream out;
-
     /////////////////////////////
     // Command Line Arguments
     /////////////////////////////
-    @Output(fullName="recal_file", shortName="recalFile", required=true, doc="Filename for the outputted covariates table recalibration file")
+    /**
+     * This algorithm treats every reference mismatch as an indication of error. However, real genetic variation is expected to mismatch the reference,
+     * so it is critical that a database of known polymorphic sites is given to the tool in order to skip over those sites.
+     */
+    @Input(fullName="knownSites", shortName = "knownSites", doc="A database of known polymorphic sites to skip over in the recalibration algorithm", required=false)
+    public List<RodBinding<Feature>> knownSites = Collections.emptyList();
+    @Output
+    PrintStream out;
+    @Output(fullName="recal_file", shortName="recalFile", required=true, doc="Filename for the output covariates table recalibration file")
     @Gather(CountCovariatesGatherer.class)
     public PrintStream RECAL_FILE;
 
@@ -124,8 +122,8 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
     /////////////////////////////
     private final RecalDataManager dataManager = new RecalDataManager(); // Holds the data HashMap, mostly used by TableRecalibrationWalker to create collapsed data hashmaps
     private final ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>(); // A list to hold the covariate objects that were requested
-    private static final double DBSNP_VS_NOVEL_MISMATCH_RATE = 2.0;        // rate at which dbSNP sites (on an individual level) mismatch relative to novel sites (determined by looking at NA12878)
-    private static int DBSNP_VALIDATION_CHECK_FREQUENCY = 1000000;                // how often to validate dbsnp mismatch rate (in terms of loci seen)
+    private static final double DBSNP_VS_NOVEL_MISMATCH_RATE = 2.0;      // rate at which dbSNP sites (on an individual level) mismatch relative to novel sites (determined by looking at NA12878)
+    private static int DBSNP_VALIDATION_CHECK_FREQUENCY = 1000000;       // how often to validate dbsnp mismatch rate (in terms of loci seen)
 
     public static class CountedData {
         private long countedSites = 0; // Number of loci used in the calculations, used for reporting in the output file
@@ -136,7 +134,7 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
 
         private long dbSNPCountsMM = 0, dbSNPCountsBases = 0;  // mismatch/base counts for dbSNP loci
         private long novelCountsMM = 0, novelCountsBases = 0;  // mismatch/base counts for non-dbSNP loci
-        private int lociSinceLastDbsnpCheck = 0;                               // loci since last dbsnp validation
+        private int lociSinceLastDbsnpCheck = 0;               // loci since last dbsnp validation
 
         /**
          * Adds the values of other to this, returning this
@@ -190,20 +188,8 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
         }
 
         // Warn the user if no dbSNP file or other variant mask was specified
-        boolean foundDBSNP = false;
-        for( ReferenceOrderedDataSource rod : this.getToolkit().getRodDataSources() ) {
-            if( rod != null ) {
-                if( rod.getType().equals(DbSNPCodec.class) ||
-                        rod.getType().equals(VCFCodec.class) ||
-                        rod.getType().equals(VCF3Codec.class) ||
-                        rod.getType().equals(BEDCodec.class) ) {
-                    foundDBSNP = true;
-                    break;
-                }
-            }
-        }
-        if( !foundDBSNP && !RUN_WITHOUT_DBSNP ) {
-            throw new UserException.CommandLineException("This calculation is critically dependent on being able to skip over known variant sites. Please provide a dbSNP ROD or a VCF file containing known sites of genetic variation.");
+        if( knownSites.isEmpty() && !RUN_WITHOUT_DBSNP ) {
+            throw new UserException.CommandLineException("This calculation is critically dependent on being able to skip over known variant sites. Please provide a VCF file containing known sites of genetic variation.");
         }
 
         // Initialize the requested covariates by parsing the -cov argument
@@ -266,12 +252,6 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
             logger.info( "\t" + cov.getClass().getSimpleName() );
             cov.initialize( RAC ); // Initialize any covariate member variables using the shared argument collection
         }
-
-//        try {
-//            stream = new PrintStream( RAC.RECAL_FILE );
-//        } catch ( FileNotFoundException e ) {
-//            throw new RuntimeException( "Couldn't open output file: ", e );
-//        }
     }
 
 
@@ -290,16 +270,13 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
      * @return Returns 1, but this value isn't used in the reduce step
      */
     public CountedData map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
-        // If any ROD covers this site then we assume it is a site of known genetic variation and we skip it
-        boolean isSNP = tracker.getNTracksWithBoundFeatures() > 0;
-        
         // Only use data from non-dbsnp sites
         // Assume every mismatch at a non-dbsnp site is indicative of poor quality
         CountedData counter = new CountedData();
-        if( !isSNP ) {
+        if( tracker.getValues(knownSites).size() == 0 ) { // If something here is in one of the knownSites tracks then skip over it, otherwise proceed
             // For each read at this locus
-            for( PileupElement p : context.getBasePileup() ) {
-                GATKSAMRecord gatkRead = (GATKSAMRecord) p.getRead();
+            for( final PileupElement p : context.getBasePileup() ) {
+                final GATKSAMRecord gatkRead = (GATKSAMRecord) p.getRead();
                 int offset = p.getOffset();
 
                 if( gatkRead.containsTemporaryAttribute( SKIP_RECORD_ATTRIBUTE  ) ) {
@@ -358,8 +335,6 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
         return counter;
     }
 
-
-
    /**
      * Update the mismatch / total_base counts for a given class of loci.
      *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index a34719b18..f61fc901b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -93,8 +93,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
 
     @Output(doc="The output BAM file", required=true)
     private StingSAMFileWriter OUTPUT_BAM = null;
-    @Argument(fullName="preserve_qscores_less_than", shortName="pQ",
-        doc="Bases with quality scores less than this threshold won't be recalibrated, default=5. In general it's unsafe to change qualities scores below < 5, since base callers use these values to indicate random or bad bases", required=false)
+    @Argument(fullName="preserve_qscores_less_than", shortName="pQ", doc="Bases with quality scores less than this threshold won't be recalibrated, default=5. In general it's unsafe to change qualities scores below < 5, since base callers use these values to indicate random or bad bases", required=false)
     private int PRESERVE_QSCORES_LESS_THAN = 5;
     @Argument(fullName="smoothing", shortName="sm", required = false, doc="Number of imaginary counts to add to each bin in order to smooth out bins with few data points, default=1")
     private int SMOOTHING = 1;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
index 74f803ac6..b2833b935 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -54,7 +54,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
-                        " -B:dbsnp,vcf " + b36dbSNP129 +
+                        " -knownSites " + b36dbSNP129 +
                         " -T CountCovariates" +
                         " -I " + bam +
                         ( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" )
@@ -135,7 +135,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
                             " -standard" +
                             " -OQ" +
                             " -recalFile %s" +
-                            " -B:dbsnp,vcf " + b36dbSNP129,
+                            " -knownSites " + b36dbSNP129,
                     1, // just one output file
                     Arrays.asList(md5));
             executeTest("testCountCovariatesUseOriginalQuals", spec);
@@ -182,7 +182,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                     "-R " + b36KGReference +
-                            " -B:dbsnp,vcf " + b36dbSNP129 +
+                            " -knownSites " + b36dbSNP129 +
                             " -T CountCovariates" +
                             " -I " + bam +
                             " -standard" +
@@ -225,30 +225,6 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
         }
     }
 
-    @Test
-    public void testCountCovariatesVCF() {
-        HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "170f0c3cc4b8d72c539136effeec9a16");
-
-        for ( Map.Entry<String, String> entry : e.entrySet() ) {
-            String bam = entry.getKey();
-            String md5 = entry.getValue();
-
-            WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                    "-R " + b36KGReference +
-                            " -B:dbsnp,VCF3 " + validationDataLocation + "vcfexample3.vcf" +
-                            " -T CountCovariates" +
-                            " -I " + bam +
-                            " -L 1:10,000,000-10,200,000" +
-                            " -standard" +
-                            " --solid_recal_mode SET_Q_ZERO" +
-                            " -recalFile %s",
-                    1, // just one output file
-                    Arrays.asList(md5));
-            executeTest("testCountCovariatesVCF", spec);
-        }
-    }
-
     @Test
     public void testCountCovariatesBED() {
         HashMap<String, String> e = new HashMap<String, String>();
@@ -260,7 +236,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                     "-R " + b36KGReference +
-                            " -B:bed,bed " + validationDataLocation + "recalibrationTest.bed" +
+                            " -knownSites:bed " + validationDataLocation + "recalibrationTest.bed" +
                             " -T CountCovariates" +
                             " -I " + bam +
                             " -L 1:10,000,000-10,200,000" +
@@ -284,10 +260,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                     "-R " + b36KGReference +
-                            " -B:anyNameABCD,VCF3 " + validationDataLocation + "vcfexample3.vcf" +
+                            " -knownSites:anyNameABCD,VCF3 " + validationDataLocation + "vcfexample3.vcf" +
                             " -T CountCovariates" +
                             " -I " + bam +
-                            " -B:dbsnp,vcf " + b36dbSNP129 +
+                            " -knownSites " + b36dbSNP129 +
                             " -L 1:10,000,000-10,200,000" +
                             " -cov ReadGroupCovariate" +
                             " -cov QualityScoreCovariate" +
@@ -312,7 +288,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                     "-R " + b36KGReference +
-                            " -B:dbsnp,vcf " + b36dbSNP129 +
+                            " -knownSites " + b36dbSNP129 +
                             " -T CountCovariates" +
                             " -I " + bam +
                             " -cov ReadGroupCovariate" +