From 61e848c4f02fc90b82a80b286055ab17dfa89a31 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 10 Sep 2010 01:47:21 +0000
Subject: [PATCH] It's clear from Sendu's calling and my own calling that
 -qScale 100.0 is a much better default value for low pass data.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4248 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/variantrecalibration/VariantRecalibrator.java  | 2 +-
 .../VariantRecalibrationWalkersIntegrationTest.java             | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index cde100a86..32e7c42a2 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -109,7 +109,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     @Argument(fullName="singleton_fp_rate", shortName="fp_rate", doc="Prior expectation that a singleton call would be a FP", required=false)
     private double SINGLETON_FP_RATE = 0.5;
     @Argument(fullName="quality_scale_factor", shortName="qScale", doc="Multiply all final quality scores by this value. Needed to normalize the quality scores.", required=false)
-    private double QUALITY_SCALE_FACTOR = 20.0;
+    private double QUALITY_SCALE_FACTOR = 100.0;
 
     /////////////////////////////
     // Private Member Variables
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index 034f9c3d5..f27ef0383 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -65,6 +65,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                                 " --ignore_filter HARD_TO_VALIDATE" +
                                 " -clusterFile " + clusterFile +
                                 " -titv 2.07" +
+                                " -qScale 20.0" + 
                                 " -o %s" +
                                 " -tranchesFile %s" +
                                 " -reportDatFile %s",