From 98a96f07c163043586826b4d511f2efdc91bca1c Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Thu, 4 Aug 2011 14:06:26 -0400 Subject: [PATCH] Updated standard deviation parameter in VQSR to our current recommended value --- .../VariantRecalibratorArgumentCollection.java | 2 +- .../VariantRecalibrationWalkersIntegrationTest.java | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java index e1a815913..28b279ccd 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java @@ -50,7 +50,7 @@ public class VariantRecalibratorArgumentCollection { @Argument(fullName="numKMeans", shortName="nKM", doc="The number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model.", required=false) public int NUM_KMEANS_ITERATIONS = 30; @Argument(fullName="stdThreshold", shortName="std", doc="If a variant has annotations more than -std standard deviations away from mean then don't use it for building the Gaussian mixture model.", required=false) - public double STD_THRESHOLD = 8.0; + public double STD_THRESHOLD = 14.0; @Argument(fullName="qualThreshold", shortName="qual", doc="If a known variant has raw QUAL value less than -qual then don't use it for building the Gaussian mixture model.", required=false) public double QUAL_THRESHOLD = 80.0; @Argument(fullName="shrinkage", shortName="shrinkage", doc="The shrinkage parameter in variational Bayes algorithm.", required=false) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java index 057053a1c..3ac7e3785 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java @@ -26,9 +26,9 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { } VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf", - "d33212a84368e821cbedecd4f59756d6", // tranches - "4652dca41222bebdf9d9fda343b2a835", // recal file - "243a397a33a935fcaccd5deb6d16f0c0"); // cut VCF + "0ddd1e0e483d2eaf56004615cea23ec7", // tranches + "58780f63182e139fdbe17f6c18b5b774", // recal file + "f67d844b6252a55452cf4167b77530b1"); // cut VCF @DataProvider(name = "VRTest") public Object[][] createData1() {