diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
index 57561a277..0d2b3478d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
@@ -4,6 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
+import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
@@ -16,10 +17,7 @@ import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 
 /**
@@ -33,8 +31,12 @@ import java.util.Map;
 public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
 
     private static final int MIN_SAMPLES = 10;
+    private Set<String> founderIds;
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+        //If available, get the founder IDs and cache them. the IC will only be computed on founders then.
+        if(founderIds == null)
+            founderIds =  ((Walker)walker).getSampleDB().getFounderIds();
         return calculateIC(vc);
     }
 
@@ -43,7 +45,7 @@ public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnno
     }
 
     private Map<String, Object> calculateIC(final VariantContext vc) {
-        final GenotypesContext genotypes = vc.getGenotypes();
+        final GenotypesContext genotypes = (founderIds == null || founderIds.isEmpty()) ? vc.getGenotypes() : vc.getGenotypes(founderIds);
         if ( genotypes == null || genotypes.size() < MIN_SAMPLES )
             return null;
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
index 7a0d78b88..80c50fd5f 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -198,4 +198,14 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         executeTest("Testing ChromosomeCounts annotation with PED file", spec);
     }
 
+    @Test
+    public void testInbreedingCoeffPed() {
+        final String MD5 = "7f1314fada5cb1f35ba1996f8a7a686b";
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf" +
+                        " -L " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf -NO_HEADER -ped " + validationDataLocation + "ug.random50000.family.ped -o %s", 1,
+                Arrays.asList(MD5));
+        executeTest("Testing InbreedingCoeff annotation with PED file", spec);
+    }
+
 }