From e73720c2db6ccfc994b75f1b9465fd3312c575f0 Mon Sep 17 00:00:00 2001 From: rpoplin Date: Tue, 3 May 2011 19:01:08 +0000 Subject: [PATCH] Updating VQSLOD annotation description git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5735 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/variantrecalibration/ApplyRecalibration.java | 2 +- .../VariantRecalibrationWalkersV2IntegrationTest.java | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ApplyRecalibration.java index 37a55ca69..3522e3a8d 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ApplyRecalibration.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ApplyRecalibration.java @@ -123,7 +123,7 @@ public class ApplyRecalibration extends RodWalker { // setup the header fields final Set hInfo = new HashSet(); hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames)); - hInfo.add(new VCFInfoHeaderLine(VariantRecalibrator.VQS_LOD_KEY, 1, VCFHeaderLineType.Float, "log10-scaled probability of variant being true under the trained gaussian mixture model")); + hInfo.add(new VCFInfoHeaderLine(VariantRecalibrator.VQS_LOD_KEY, 1, VCFHeaderLineType.Float, "log odds ratio of being a true variant versus being false under the trained gaussian mixture model")); final TreeSet samples = new TreeSet(); samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames)); diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersV2IntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersV2IntegrationTest.java index 7d923e21a..da00b6ee9 100755 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersV2IntegrationTest.java +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersV2IntegrationTest.java @@ -27,7 +27,7 @@ public class VariantRecalibrationWalkersV2IntegrationTest extends WalkerTest { VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf", "920b12d7765eb4f6f4a1bab045679b31", // tranches "41bbc5f07c8a9573d5bb638f01808bba", // recal file - "2b8c5e884bf5a739b782f5b3bf17f19c"); // cut VCF + "d9aa7a0f8fb886df4394f1636605adca"); // cut VCF @DataProvider(name = "VRTest") public Object[][] createData1() { @@ -43,7 +43,7 @@ public class VariantRecalibrationWalkersV2IntegrationTest extends WalkerTest { " -B:dbsnp,VCF,known=true,training=false,truth=false,prior=10.0 " + GATKDataLocation + "dbsnp_132_b37.leftAligned.vcf" + " -B:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 " + comparisonDataLocation + "Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf" + " -B:omni,VCF,known=false,training=true,truth=true,prior=12.0 " + comparisonDataLocation + "Validated/Omni2.5_chip/Omni25_sites_1525_samples.b37.vcf" + - " -T ContrastiveRecalibrator" + + " -T VariantRecalibrator" + " -B:input,VCF " + params.inVCF + " -L 20:1,000,000-40,000,000" + " -an QD -an HaplotypeScore -an HRun" +