From 28cfb06513e79085540c86f5f5cddb149154d08c Mon Sep 17 00:00:00 2001 From: Laura Gauthier Date: Fri, 12 Feb 2016 20:32:06 -0500 Subject: [PATCH] Add AS_culprit and AS_VQSLOD to VCF header in ApplyRecalibration so output passes VCF validation --- .../walkers/variantrecalibration/ApplyRecalibration.java | 2 ++ .../VariantRecalibrationWalkersIntegrationTest.java | 4 ++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java index 7474ecb1f..9cdbc8298 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java @@ -328,6 +328,8 @@ public class ApplyRecalibration extends RodWalker implements T public static void addAlleleSpecificVQSRHeaderLines(final Set hInfo) { hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_FILTER_STATUS_KEY)); + hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_CULPRIT_KEY)); + hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_VQS_LOD_KEY)); } /** diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java index 4ef98620e..89b7cb8ba 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java @@ -359,7 +359,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { " -tranchesFile " + privateTestDir + "VQSR.AStest.snps.tranches" + " -recalFile " + privateTestDir + "VQSR.AStest.snps.recal"; - final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("db465aaf18b9de8b3191de63fc9f0e6e")); + final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("cd087f2824fac5fe04c6c50cbdab1fab")); final List outputFiles = executeTest("testApplyRecalibrationAlleleSpecificSNPmode", spec).getFirst(); setPDFsForDeletion(outputFiles); } @@ -377,7 +377,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { " -tranchesFile " + privateTestDir + "VQSR.AStest.indels.tranches" + " -recalFile " + privateTestDir + "VQSR.AStest.indels.recal"; - final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("7c1df91b9827a5906d30db52e96922e1")); + final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("b0d14f1c0647f46819018cd378036024")); final List outputFiles = executeTest("testApplyRecalibrationAlleleSpecificINDELmode", spec).getFirst(); setPDFsForDeletion(outputFiles); }