From 28805d17ca4390eaac5da679bdc2e38b4dfbaa40 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 22 Nov 2010 16:48:08 +0000
Subject: [PATCH] Commenting out allele-balance for now.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4715 348d0f76-0448-11de-a6fe-93d51630548a
---
 scala/qscript/fullCallingPipeline.q | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q
index 060cf588c..7a700fdbf 100755
--- a/scala/qscript/fullCallingPipeline.q
+++ b/scala/qscript/fullCallingPipeline.q
@@ -311,8 +311,10 @@ class fullCallingPipeline extends QScript {
     handFilter.jobOutputFile = new File(".queue/logs/SNPCalling/HandFilter.out")
     handFilter.variantVCF = masker.out
     handFilter.rodBind :+= RodBind("mask", "VCF", mergeIndels.out)
-    handFilter.filterName ++= List("StrandBias","AlleleBalance","QualByDepth","HomopolymerRun")
-    handFilter.filterExpression ++= List("\"SB>=0.10\"","\"AB>=0.75\"","\"QD<5.0\"","\"HRun>=4\"")
+    //handFilter.filterName ++= List("StrandBias","AlleleBalance","QualByDepth","HomopolymerRun")
+    //handFilter.filterExpression ++= List("\"SB>=0.10\"","\"AB>=0.75\"","\"QD<5.0\"","\"HRun>=4\"")
+    handFilter.filterName ++= List("StrandBias","QualByDepth","HomopolymerRun")
+    handFilter.filterExpression ++= List("\"SB>=0.10\"","\"QD<5.0\"","\"HRun>=4\"")
     handFilter.out = swapExt("SnpCalls",annotated.out,".vcf",".handfiltered.vcf")
     handFilter.analysisName = base+"_HandFilter"