From 72f4cf9c0ecbd8608d207ee59a5e5bd36a395be8 Mon Sep 17 00:00:00 2001
From: Menachem Fromer <fromer@broadinstitute.org>
Date: Fri, 15 Jul 2011 17:44:31 -0400
Subject: [PATCH] Walker to perform deterministic annotation of phasing by
 transmission (to be compatible with RBP's definition of consecutive pairwise
 phasing)

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

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index 1d9616aac..fbe6e5b5a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -242,7 +242,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         return new PhasingStatsAndOutput(phaseStats, completedList);
     }
 
-    private static final Set<String> KEYS_TO_KEEP_IN_REDUCED_VCF = new HashSet<String>(Arrays.asList("PQ"));
+    private static final Set<String> KEYS_TO_KEEP_IN_REDUCED_VCF = new HashSet<String>(Arrays.asList(PQ_KEY));
 
     private VariantContext reduceVCToSamples(VariantContext vc, List<String> samplesToPhase) {
 //        for ( String sample : samplesToPhase )