diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/Alignability.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/Alignability.java
index 8fdc97189..7058f9701 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/Alignability.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/Alignability.java
@@ -20,17 +20,14 @@ public class Alignability implements InfoFieldAnnotation {
 						   VariantContext vc)
 	{
 		TabularROD record = (TabularROD)(tracker.lookup("alignability", null));
-		int value;
-		if (record == null) { value = 3; }
-		else 
-		{ 
-			if (record.get("alignability") == null) 
-			{ 
-				throw new RuntimeException("ERROR: alignability column not defined in alignability input.\n");
-			}
-			value = Integer.parseInt(record.get("alignability")); 
-		}
-        
+		if (record == null)
+            return null;
+
+        if (record.get("alignability") == null)
+            throw new RuntimeException("ERROR: alignability column not defined in alignability input.\n");
+
+        int value = Integer.parseInt(record.get("alignability"));
+
         Map<String, Object> map = new HashMap<String, Object>();
         map.put(getKeyName(), String.format("%d", value));
         return map;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
index 2fafa1b2e..eb0a62795 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -8,7 +8,6 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.genotype.vcf.*;
-import org.broadinstitute.sting.utils.genotype.Genotype;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import java.util.*;
@@ -54,6 +53,10 @@ public class VariantAnnotator extends LocusWalker<Integer, Integer> {
         for (int i = 0; i < genotypeAnnotationClasses.size(); i++)
             out.println("\t" + genotypeAnnotationClasses.get(i).getSimpleName());
         out.println();
+        out.println("\nAvailable classes/groups of annotations:");
+        for ( Class c : PackageUtils.getInterfacesExtendingInterface(AnnotationType.class) )
+            out.println("\t" + c.getSimpleName());
+        out.println();
         System.exit(0);
     }
 
@@ -168,12 +171,4 @@ public class VariantAnnotator extends LocusWalker<Integer, Integer> {
 
         vcfWriter.close();
     }
-
-    public static Genotype getFirstVariant(char ref, List<Genotype> genotypes) {
-        for ( Genotype g : genotypes ) {
-            if ( g.isVariant(ref) )
-                return g;
-        }
-        return null;
-    }
 }