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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
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rpoplin 2010-09-10 01:47:21 +00:00
parent e183b6598c
commit 61e848c4f0
2 changed files with 2 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -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) @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; 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) @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 // Private Member Variables

1
java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
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@ -65,6 +65,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" --ignore_filter HARD_TO_VALIDATE" + " --ignore_filter HARD_TO_VALIDATE" +
" -clusterFile " + clusterFile + " -clusterFile " + clusterFile +
" -titv 2.07" + " -titv 2.07" +
" -qScale 20.0" +
" -o %s" + " -o %s" +
" -tranchesFile %s" + " -tranchesFile %s" +
" -reportDatFile %s", " -reportDatFile %s",