diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java
index 350020111..0b2187dcd 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java
@@ -63,6 +63,53 @@ public class GenomicAnnotation implements InfoFieldAnnotation {
     /** Replacement for each character in ILLEGAL_INFO_FIELD_VALUES */
     public static final char[] ILLEGAL_INFO_FIELD_VALUE_SUBSTITUTES = {  '_', '-',  '!'  };
 
+
+    private void modifyAnnotationsForIndels(VariantContext vc, String featureName, Map<String, String> annotationsForRecord) {
+        String inCodingRegionKey = featureName + ".inCodingRegion";
+        String referenceCodonKey = featureName + ".referenceCodon";
+        String variantCodonKey = featureName + ".variantCodon";
+        String codingCoordStrKey = featureName + ".codingCoordStr";
+        String proteinCoordStrKey = featureName + ".proteinCoordStr";
+        String haplotypeReferenceKey = featureName + "." + HAPLOTYPE_REFERENCE_COLUMN;
+        String haplotypeAlternateKey = featureName + "." + HAPLOTYPE_ALTERNATE_COLUMN;
+        String functionalClassKey = featureName + ".functionalClass";
+        String startKey = featureName + "." + START_COLUMN;
+        String endKey = featureName + "." + END_COLUMN;
+        String referenceAAKey = featureName + ".referenceAA";
+        String variantAAKey = featureName + ".variantAA";
+        String changesAAKey = featureName + ".changesAA";
+
+        annotationsForRecord.put(variantCodonKey, "unknown");
+        annotationsForRecord.put(codingCoordStrKey, "unknown");
+        annotationsForRecord.put(proteinCoordStrKey, "unknown");
+        annotationsForRecord.put(referenceAAKey, "unknown");
+        annotationsForRecord.put(variantAAKey, "unknown");
+
+        String refAllele = vc.getReference().getDisplayString();
+        if (refAllele.length() == 0) { refAllele = "-"; }
+
+        String altAllele = vc.getAlternateAllele(0).toString();
+        if (altAllele.length() == 0) { altAllele = "-"; }
+
+        annotationsForRecord.put(haplotypeReferenceKey, refAllele);
+        annotationsForRecord.put(haplotypeAlternateKey, altAllele);
+        annotationsForRecord.put(startKey, String.format("%d", vc.getStart()));
+        annotationsForRecord.put(endKey, String.format("%d", vc.getEnd()));
+
+        boolean isCodingRegion = annotationsForRecord.containsKey(inCodingRegionKey) && annotationsForRecord.get(inCodingRegionKey).equalsIgnoreCase("true") ? true : false;
+        boolean isFrameshift = (vc.getIndelLengths().get(0) % 3 == 0) ? false : true;
+
+        String functionalClass;
+        if (isCodingRegion) {
+            functionalClass = isFrameshift ? "frameshift" : "inframe";
+            annotationsForRecord.put(changesAAKey, "true");
+        } else {
+            functionalClass = "noncoding";
+        }
+
+        annotationsForRecord.put(functionalClassKey, functionalClass);
+    }
+
     /**
      * For each -B input file, for each record which overlaps the current locus, generates a
      * set of annotations of the form:
@@ -170,6 +217,10 @@ public class GenomicAnnotation implements InfoFieldAnnotation {
                 }
             }
 
+            if (vc.isIndel()) {
+                modifyAnnotationsForIndels(vc, name, annotationsForRecord);
+            }
+
             //filters passed, so add this record.
             List<Map<String, String>> listOfMatchingRecords = (List<Map<String, String>>) annotations.get( name );
             if(listOfMatchingRecords == null) {
diff --git a/java/test/org/broadinstitute/sting/WalkerTest.java b/java/test/org/broadinstitute/sting/WalkerTest.java
index 84ce40029..5d4346427 100755
--- a/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -71,6 +71,20 @@ public class WalkerTest extends BaseTest {
         return md5s;
     }
 
+    public String cmdLineBuilder(String ... arguments) {
+        String cmdline = "";
+
+        for ( int argIndex = 0; argIndex < arguments.length; argIndex++ ) {
+            cmdline += arguments[argIndex];
+
+            if (argIndex < arguments.length - 1) {
+                cmdline += " ";
+            }
+        }
+
+        return cmdline;
+    }
+
     public class WalkerTestSpec {
         String args = "";
         int nOutputFiles = -1;
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java
index 369624c6b..223307dc4 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java
@@ -6,8 +6,10 @@ import java.util.Arrays;
 import org.broadinstitute.sting.WalkerTest;
 import org.testng.annotations.Test;
 
-public class
-        GenomicAnnotatorIntegrationTest extends WalkerTest {
+public class GenomicAnnotatorIntegrationTest extends WalkerTest {
+    String testFileWithIndels = validationDataLocation + "/GenomicAnnotatorValidation/1KGBroadWEx.cleaned.indels.vcf";
+    String testFileWithSNPsAndIndels = validationDataLocation + "/GenomicAnnotatorValidation/1KGBroadWEx.variants.vcf";
+
     @Test
     public void testGenomicAnnotatorOnDbSNP() {
 
@@ -42,4 +44,38 @@ public class
         executeTest("test with dbSNP and -s arg", specWithSArg);
 
     }
+
+    @Test
+    public void testGenomicAnnotatorOnIndels() {
+        WalkerTestSpec testOnIndels = new WalkerTestSpec(
+                cmdLineBuilder(
+                        "-T GenomicAnnotator",
+                        "-R " + b37KGReference,
+                        "-L 22:10000000-20000000",
+                        "-B:refseq,AnnotatorInputTable " + b37Refseq,
+                        "-B:variant,VCF " + testFileWithIndels,
+                        "-o %s"
+                ),
+                1,
+                Arrays.asList("1f8189433e87cc0b986cddb6a9a74585")
+        );
+        executeTest("testGenomicAnnotatorOnIndels", testOnIndels);
+    }
+
+    @Test
+    public void testGenomicAnnotatorOnSNPsAndIndels() {
+        WalkerTestSpec testOnSNPsAndIndels = new WalkerTestSpec(
+                cmdLineBuilder(
+                        "-T GenomicAnnotator",
+                        "-R " + b37KGReference,
+                        "-L 22:10000000-20000000",
+                        "-B:refseq,AnnotatorInputTable " + b37Refseq,
+                        "-B:variant,VCF " + testFileWithSNPsAndIndels,
+                        "-o %s"
+                ),
+                1,
+                Arrays.asList("e9e93fb1d2700e000bd0e9493524dc4c")
+        );
+        executeTest("testGenomicAnnotatorOnSNPsAndIndels", testOnSNPsAndIndels);
+    }
 }
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
index 6fd8bddc6..fbbfa297a 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -27,6 +27,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
 
     private static String[] testsEnumerations = {root, rootGZ};
 
+    /*
     private String cmdLineBuilder(String ... arguments) {
         String cmdline = "";
 
@@ -40,6 +41,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
 
         return cmdline;
     }
+    */
 
     @Test
     public void testFundamentalsCountVariantsSNPsAndIndels() {