From b3ac47812caf4c628215a69b3214b6c8836f826a Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 20 Dec 2010 16:43:50 +0000
Subject: [PATCH] No longer emits records at filtered sites, in sub-sampling
 mode

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4883 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index edb6ec6e8..0d8fdb69f 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -1008,7 +1008,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
     }
 
     private void writeVCF(VariantContext vc) {
-        if ( samplesToPhase == null || vc.isVariant() ) // if we are only operating on specific samples, don't write out all sites, just those where the VC is variant
+        if ( samplesToPhase == null || (vc.isVariant() && vc.isNotFiltered())) // if we are only operating on specific samples, don't write out all sites, just those where the VC is variant
             WriteVCF.writeVCF(vc, writer, logger);
     }