diff --git a/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java b/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
index fa154fca3..dd12ce761 100755
--- a/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
@@ -25,12 +25,14 @@
 
 package org.broadinstitute.sting.utils.classloader;
 
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.reflections.util.ClasspathHelper;
 
 import java.io.File;
 import java.io.IOException;
+import java.lang.annotation.Annotation;
 import java.lang.reflect.*;
 import java.net.URL;
 import java.util.*;
@@ -234,4 +236,17 @@ public class JVMUtils {
         } else
             throw new ReviewedStingException("BUG: could not find generic type on class " + t);
     }
+
+    /**
+     * Returns a comma-separated list of the names of the interfaces implemented by this class
+     *
+     * @param covClass
+     * @return
+     */
+    public static String classInterfaces(final Class covClass) {
+        final List<String> interfaces = new ArrayList<String>();
+        for ( final Class interfaceClass : covClass.getInterfaces() )
+            interfaces.add(interfaceClass.getSimpleName());
+        return Utils.join(", ", interfaces);
+    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
index 2d05877af..8a9143c89 100644
--- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
@@ -29,6 +29,7 @@ import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.report.GATKReport;
 import org.broadinstitute.sting.gatk.report.GATKReportTable;
 import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.recalibration.covariates.*;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.R.RScriptExecutor;
@@ -117,6 +118,12 @@ public class RecalUtils {
 
         if (argumentCollection.COVARIATES != null) {                                                                    // parse the -cov arguments that were provided, skipping over the ones already specified
             for (String requestedCovariateString : argumentCollection.COVARIATES) {
+                // help the transition from BQSR v1 to BQSR v2
+                if ( requestedCovariateString.equals("DinucCovariate") )
+                    throw new UserException.CommandLineException("DinucCovariate has been retired.  Please use its successor covariate " +
+                            "ContextCovariate instead, which includes the 2 bp (dinuc) substitution model of the retired DinucCovariate " +
+                            "as well as an indel context to model the indel error rates");
+
                 boolean foundClass = false;
                 for (Class<? extends Covariate> covClass : covariateClasses) {
                     if (requestedCovariateString.equalsIgnoreCase(covClass.getSimpleName())) {                          // -cov argument matches the class name for an implementing class
@@ -178,18 +185,18 @@ public class RecalUtils {
         return dest;
     }
 
-    public static void listAvailableCovariates(Logger logger) {
-        // Get a list of all available covariates
-        final List<Class<? extends Covariate>> covariateClasses = new PluginManager<Covariate>(Covariate.class).getPlugins();
-
-        // Print and exit if that's what was requested
+    /**
+     * Print a list of all available covariates to logger as info
+     *
+     * @param logger
+     */
+    public static void listAvailableCovariates(final Logger logger) {
         logger.info("Available covariates:");
-        for (Class<?> covClass : covariateClasses)
-            logger.info(covClass.getSimpleName());
-        logger.info("");
+        for (final Class<? extends Covariate> covClass : new PluginManager<Covariate>(Covariate.class).getPlugins()) {
+            logger.info(String.format("\t%30s\t%s", covClass.getSimpleName(), JVMUtils.classInterfaces(covClass)));
+        }
     }
 
-
     public enum SOLID_RECAL_MODE {
         /**
          * Treat reference inserted bases as reference matching bases. Very unsafe!
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/BinaryTagCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/BinaryTagCovariate.java
deleted file mode 100644
index cebdebf9d..000000000
--- a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/BinaryTagCovariate.java
+++ /dev/null
@@ -1,63 +0,0 @@
-package org.broadinstitute.sting.utils.recalibration.covariates;
-
-import org.broadinstitute.sting.utils.recalibration.ReadCovariates;
-import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-
-/**
- * Binary covariate allows BQSR to recalibrate based on a binary covariate in the BAM file. This covariate should assume values of 1 and 0.
- *
- * @author Mauricio Carneiro
- * @since 7/6/12
- */
-public class BinaryTagCovariate implements ExperimentalCovariate {
-
-    private String tag;
-
-    @Override
-    public void initialize(RecalibrationArgumentCollection RAC) {
-        tag = RAC.BINARY_TAG_NAME;
-    }
-
-    @Override
-    public void recordValues(GATKSAMRecord read, ReadCovariates values) {
-        final Object tagObject = read.getAttribute(tag);
-
-        byte[] binaryTag;
-        if (tagObject instanceof byte[])
-            binaryTag = (byte[]) tagObject;
-        else if (tagObject instanceof String) {
-            int readLength = ((String) tagObject).length();
-            binaryTag = new byte[readLength];
-            for (int i = 0; i<readLength; i++)
-                binaryTag[i] = Byte.decode(((String) tagObject).substring(i, i+1));
-        }
-        else
-            throw new UserException("Binary tag is not a byte array (fast) or a string (slow). Type not supported");
-
-        for (int i = 0; i < read.getReadLength(); i++) {
-            values.addCovariate((int) binaryTag[i], (int) binaryTag[i], (int) binaryTag[i], i);
-        }
-    }
-
-    @Override
-    public Object getValue(String str) {
-        return Integer.decode(str);
-    }
-
-    @Override
-    public String formatKey(int key) {
-        return String.format("%d", key);
-    }
-
-    @Override
-    public int keyFromValue(Object value) {
-        return Integer.decode((String) value);
-    }
-
-    @Override
-    public int maximumKeyValue() {
-        return 1;
-    }
-}