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Merged bug fix from Stable into Unstable

This commit is contained in:
Ryan Poplin 2011-08-07 17:39:03 -04:00
parent b3e57c329a 738e94efcb
commit 6693407bd8
3 changed files with 7 additions and 4 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
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@ -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)

6
public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
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@ -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() {

3
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
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@ -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
//