diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
index f3f2fe664..ea7a3d3d4 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
@@ -125,7 +125,7 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
     }
 
     /**
-     * given a existing file, open it and append all the valid triplet lines to an existing list
+     * given an existing file, open it and append all the valid triplet lines to an existing list
      *
      * @param rodTripletList the list of existing triplets
      * @param filename       the file to attempt to extract ROD triplets from
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
index b814db015..90e002362 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
@@ -4,6 +4,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.RODRecordList;
+import org.broadinstitute.sting.gatk.refdata.VariationRod;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
@@ -103,7 +104,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
     private long solidInsertedReferenceBases = 0; // Number of bases where we believe SOLID has inserted the reference because the color space is inconsistent with the read base
     private long otherColorSpaceInconsistency = 0; // Number of bases where the color space is inconsistent with the read but the reference wasn't inserted.
     private int numUnprocessed = 0; // Number of consecutive loci skipped because we are only processing every Nth site
-    private static final String versionString = "v2.2.4"; // Major version, minor version, and build number
+    private static final String versionString = "v2.2.5"; // Major version, minor version, and build number
     private Pair<Long, Long> dbSNP_counts = new Pair<Long, Long>(0L, 0L);  // mismatch/base counts for dbSNP loci
     private Pair<Long, Long> novel_counts = new Pair<Long, Long>(0L, 0L);  // mismatch/base counts for non-dbSNP loci
     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)
@@ -149,8 +150,9 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
         // Warn the user if no dbSNP file was specified
         boolean foundDBSNP = false;
         for( ReferenceOrderedDataSource rod : this.getToolkit().getRodDataSources() ) {
-            if( rod.getName().equalsIgnoreCase( "dbsnp" ) ) {
+            if( rod != null ) {
                 foundDBSNP = true;
+                break;
             }
         }
         if( !foundDBSNP ) {
@@ -232,15 +234,12 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
      */
     public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
 
-        // Pull out anything passed by -B name,type,file that has the name "dbsnp"
-        final RODRecordList<ReferenceOrderedDatum> dbsnpRODs = tracker.getTrackData( "dbsnp", null );
+        // Pull out data for this locus for all the input RODs and check if this is a known variant site in any of them
         boolean isSNP = false;
-        if (dbsnpRODs != null) {
-            for( ReferenceOrderedDatum rod : dbsnpRODs ) {
-                if( ((Variation)rod).isSNP() ) {
-                    isSNP = true; // At least one of the rods says this is a snp site
-                    break;
-                }
+        for( ReferenceOrderedDatum rod : tracker.getAllRods() ) {
+            if( rod != null && rod instanceof Variation && ((Variation)rod).isSNP() ) {
+                isSNP = true; // At least one of the rods says this is a snp site
+                break;
             }
         }
 
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
index 09c4ce095..65ad18d84 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -133,6 +133,34 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
         }
     }
 
+    @Test
+    public void testCountCovariatesVCFPlusDBsnp() {
+        HashMap<String, String> e = new HashMap<String, String>();
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "cc1cc9c1ff184d388d81574fdccc608e");
+
+        for ( Map.Entry<String, String> entry : e.entrySet() ) {
+            String bam = entry.getKey();
+            String md5 = entry.getValue();
+
+            WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                    "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                            " -B anyNameABCD,VCF," + validationDataLocation + "vcfexample3.vcf" +
+                            " -T CountCovariates" +
+                            " -I " + bam +
+                            " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
+                            " -L 1:10,000,000-10,200,000" +
+                            " -cov ReadGroupCovariate" +
+                            " -cov QualityScoreCovariate" +
+                            " -cov CycleCovariate" +
+                            " -cov DinucCovariate" +
+                            " --solid_recal_mode SET_Q_ZERO" +
+                            " -recalFile %s",
+                    1, // just one output file
+                    Arrays.asList(md5));
+            executeTest("testCountCovariatesVCFPlusDBsnp", spec);
+        }
+    }
+
     @Test
     public void testCountCovariatesNoReadGroups() {
         HashMap<String, String> e = new HashMap<String, String>();