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Updating VQSLOD annotation description 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5735 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-05-03 19:01:08 +00:00
parent 11052918d9
commit e73720c2db
2 changed files with 3 additions and 3 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ApplyRecalibration.java
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@ -123,7 +123,7 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
// setup the header fields
final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
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<String> samples = new TreeSet<String>();
samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames));

4
java/test/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersV2IntegrationTest.java
View File

@ -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" +