diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java
index 216d43a21..387c26021 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java
@@ -92,7 +92,9 @@ public class VariantsToBinaryPedIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString("NA12878.subset.vcf", "CEUTrio.NA12878.fam",10),
                 3,
-                Arrays.asList("411ef932095728bfa5e509c2c0e4cfa8","daf853d2fcbfc77daa1f9ae190be24f4","02f1c462ebc8576e399d0e94f729fd95")
+                Arrays.asList("411ef932095728bfa5e509c2c0e4cfa8",
+		"98f955f8b2af0aef58c96cc0cde66662",
+		"02f1c462ebc8576e399d0e94f729fd95")
         );
 
         executeTest(testName, spec);
@@ -182,7 +184,9 @@ public class VariantsToBinaryPedIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString("CEUTrio.subset.vcf", "CEUTrio.fam",10),
                 3,
-                Arrays.asList("59b93fbb4bb31309b3adc83ba96dd1a2","3bfb01c17935e3d194d266755b446e82","7887d2e0bf605dbcd0688c552cdb99d5")
+                Arrays.asList("59b93fbb4bb31309b3adc83ba96dd1a2",
+		"cbef0432e78f0a31a3cb4cd1942ada62",
+		"7887d2e0bf605dbcd0688c552cdb99d5")
         );
 
         executeTest(testName, spec);
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java
index b57f187b9..8618d816d 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java
@@ -488,8 +488,8 @@ public class VariantsToBinaryPed extends RodWalker<Integer,Integer> {
                     }
                     String sid = famSplit[1];
                     String fid = famSplit[0];
-                    String mom = famSplit[2];
-                    String dad = famSplit[3];
+                    String dad = famSplit[2];
+                    String mom = famSplit[3];
                     String sex = famSplit[4];
                     String pheno = famSplit[5];
                     HashMap<String,String> values = new HashMap<String, String>();