From 0111505ea9e2e3df4c8e5ce3553df45cd0e64eca Mon Sep 17 00:00:00 2001
From: Christopher Hartl <chartl@broadinstitute.org>
Date: Thu, 2 Feb 2012 11:41:16 -0500
Subject: [PATCH] Terrible. Swapping the paternal and sample ids.

---
 .../sting/gatk/walkers/variantutils/VariantsToPed.java          | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToPed.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToPed.java
index 32b2dd06c..aab230b69 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToPed.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToPed.java
@@ -114,7 +114,7 @@ public class VariantsToPed extends RodWalker<Integer,Integer> {
                 String mid = mVals.containsKey("mom") ? mVals.get("mom") : String.format("dummy_%d",++dummyID);
                 String sex = mVals.containsKey("sex") ? mVals.get("sex") : "3";
                 String pheno = mVals.get("phenotype");
-                outFam.printf("%s\t%s\t%s\t%s\t%s\t%s%n",fid,pid,sample,mid,sex,pheno);
+                outFam.printf("%s\t%s\t%s\t%s\t%s\t%s%n",fid,sample,pid,mid,sex,pheno);
             }
         }
     }