From 6ec686b8779770a99b9aa8cd3aa27bcc6de0c8d9 Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Mon, 6 Feb 2012 13:19:26 -0500
Subject: [PATCH] Complement to previous commit: make sure we also don't
 inherit filter from input VCF when genotyping at an empty site

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

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 5cdef6cf5..aae781628 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -252,7 +252,7 @@ public class UnifiedGenotyperEngine {
             VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, ref, rawContext.getLocation(), false, logger, UAC.alleles);
             if ( vcInput == null )
                 return null;
-            vc = new VariantContextBuilder(vcInput).source("UG_call").noID().referenceBaseForIndel(ref.getBase()).attributes(new HashMap<String, Object>()).make();
+            vc = new VariantContextBuilder(vcInput).source("UG_call").noID().referenceBaseForIndel(ref.getBase()).attributes(new HashMap<String, Object>()).filters(new HashSet<String>()).make();
         } else {
             // deal with bad/non-standard reference bases
             if ( !Allele.acceptableAlleleBases(new byte[]{ref.getBase()}) )