From 67f15896527ad0bfdc000498fdb0268f35e44fbb Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 8 Jul 2010 22:48:30 +0000
Subject: [PATCH] --fdr_filter_level isn't mandatory

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3748 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/variantrecalibration/ApplyVariantCuts.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
index b58e5ce18..8f1ba6c2d 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
@@ -65,7 +65,7 @@ public class ApplyVariantCuts extends RodWalker<Integer, Integer> {
     private String TRANCHE_FILENAME = "optimizer.dat.tranches";
     @Argument(fullName="outputVCFFile", shortName="outputVCF", doc="The output filtered VCF file", required=true)
     private String OUTPUT_FILENAME = "optimizer.vcf";
-    @Argument(fullName="fdr_filter_level", shortName="fdr_filter_level", doc="The FDR level at which to start filtering.", required=true)
+    @Argument(fullName="fdr_filter_level", shortName="fdr_filter_level", doc="The FDR level at which to start filtering.", required=false)
     private double FDR_FILTER_LEVEL = 0.0;