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() { diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala index 934cf2a3c..4f1fe741a 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala @@ -134,6 +134,9 @@ class GATKResourcesBundle extends QScript { addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf", "1000G_indels_for_realignment", b37, true, false)) + addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Mills_Devine_Indels_2011/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.vcf", + "indels_mills_devine", b37, true, true)) + // // example call set for wiki tutorial //