diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
similarity index 52%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
index c67d829c2..a5c2b32f0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
@@ -15,9 +15,9 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import java.util.*;
 
 /**
- * Rough category of indel type (insertion, deletion, multi-allelic, other)
+ * Assigns a roughly correct category of the variant type (SNP, MNP, insertion, deletion, etc.)
  */
-public class IndelType extends InfoFieldAnnotation implements ExperimentalAnnotation {
+public class VariantType extends InfoFieldAnnotation implements ExperimentalAnnotation {
 
     public Map<String, Object> annotate(final RefMetaDataTracker tracker,
                                         final AnnotatorCompatible walker,
@@ -26,41 +26,35 @@ public class IndelType extends InfoFieldAnnotation implements ExperimentalAnnota
                                         final VariantContext vc,
                                         final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
 
-        int run;
-        if (vc.isMixed()) {
-            Map<String, Object> map = new HashMap<String, Object>();
-            map.put(getKeyNames().get(0), String.format("%s", "MIXED"));
-            return map;
-
-        }
-        else if ( vc.isIndel() ) {
-            String type="";
-            if (!vc.isBiallelic())
-                type = "MULTIALLELIC_INDEL";
-            else {
-                if (vc.isSimpleInsertion())
-                    type = "INS.";
-                else if (vc.isSimpleDeletion())
-                    type = "DEL.";
-                else
-                    type = "OTHER.";
-                ArrayList<Integer> inds = IndelUtils.findEventClassificationIndex(vc, ref);
-                for (int k : inds) {
-                    type = type+ IndelUtils.getIndelClassificationName(k)+".";
-                }
-            }
-            Map<String, Object> map = new HashMap<String, Object>();
-            map.put(getKeyNames().get(0), String.format("%s", type));
-            return map;
+        StringBuffer type = new StringBuffer("");
+        if ( vc.isVariant() && !vc.isBiallelic() )
+            type.append("MULTIALLELIC_");
 
+        if ( !vc.isIndel() ) {
+            type.append(vc.getType().toString());
         } else {
-            return null;
+            if (vc.isSimpleInsertion())
+                type.append("INSERTION.");
+            else if (vc.isSimpleDeletion())
+                type.append("DELETION.");
+            else
+                type.append("COMPLEX.");
+            ArrayList<Integer> inds = IndelUtils.findEventClassificationIndex(vc, ref);
+            type.append(IndelUtils.getIndelClassificationName(inds.get(0)));
+
+            for (int i = 1; i < inds.size(); i++ ) {
+                type.append(".");
+                type.append(IndelUtils.getIndelClassificationName(inds.get(i)));
+            }
         }
 
+        Map<String, Object> map = new HashMap<String, Object>();
+        map.put(getKeyNames().get(0), String.format("%s", type));
+        return map;
     }
 
-    public List<String> getKeyNames() { return Arrays.asList("IndelType"); }
+    public List<String> getKeyNames() { return Arrays.asList("VariantType"); }
 
-    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("IndelType", 1, VCFHeaderLineType.String, "Indel type description")); }
+    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("VariantType", 1, VCFHeaderLineType.String, "Variant type description")); }
 
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java b/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java
index c6ca39f4b..9b1cc9733 100755
--- a/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java
@@ -122,9 +122,9 @@ public class IndelUtils {
 
         ArrayList<Integer> inds = new ArrayList<Integer>();
         if ( vc.isSimpleInsertion() ) {
-            indelAlleleString = vc.getAlternateAllele(0).getDisplayString();
+            indelAlleleString = vc.getAlternateAllele(0).getDisplayString().substring(1);
         } else if ( vc.isSimpleDeletion() ) {
-            indelAlleleString = vc.getReference().getDisplayString();
+            indelAlleleString = vc.getReference().getDisplayString().substring(1);
         }
         else {
             inds.add(IND_FOR_OTHER_EVENT);