From fac082de64762732cbea08ddc3a47f6a41e47014 Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Sun, 3 Jul 2011 14:32:12 -0400
Subject: [PATCH] Report only highest AF and AC in multiallelic records in
 VariantsToTable or else R can't parse table

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

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
index 2111b0959..d8340b761 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
@@ -170,7 +170,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
                 throw new UserException(String.format("Missing field %s in vc %s at %s", field, vc.getSource(), vc));
             }
 
-            if (field.equals("AF")) {
+            if (field.equals("AF") || field.equals("AC")) {
                      String afo = val;
 
                      double af=0;