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Add AS_culprit and AS_VQSLOD to VCF header in ApplyRecalibration so output passes VCF validation

This commit is contained in:
Laura Gauthier 2016-02-12 20:32:06 -05:00
parent dcc6c0f2aa
commit 28cfb06513
2 changed files with 4 additions and 2 deletions
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2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java
View File

@ -328,6 +328,8 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
public static void addAlleleSpecificVQSRHeaderLines(final Set<VCFHeaderLine> 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));
}
/**

4
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -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<File> 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<File> outputFiles = executeTest("testApplyRecalibrationAlleleSpecificINDELmode", spec).getFirst();
setPDFsForDeletion(outputFiles);
}