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We now allow arbitrary annotations other than dbSNP (e.g. HM3) to come out of the Unified Genotyper. This was already set up in the Variant Annotator Engine and was just a matter of hooking UG up to it. Added integration test to ensure correct behavior.

This commit is contained in:
Eric Banks 2012-04-10 12:30:35 -04:00
parent ec9822b2a7
commit 10e74a71eb
2 changed files with 20 additions and 1 deletions
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13
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -127,8 +127,19 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
@ArgumentCollection
protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
public RodBinding<VariantContext> getDbsnpRodBinding() { return dbsnp.dbsnp; }
/**
* If a call overlaps with a record from the provided comp track, the INFO field will be annotated
* as such in the output with the track name (e.g. -comp:FOO will have 'FOO' in the INFO field).
* Records that are filtered in the comp track will be ignored.
* Note that 'dbSNP' has been special-cased (see the --dbsnp argument).
*/
@Input(fullName="comp", shortName = "comp", doc="comparison VCF file", required=false)
public List<RodBinding<VariantContext>> comps = Collections.emptyList();
public List<RodBinding<VariantContext>> getCompRodBindings() { return comps; }
// The following are not used by the Unified Genotyper
public RodBinding<VariantContext> getSnpEffRodBinding() { return null; }
public List<RodBinding<VariantContext>> getCompRodBindings() { return Collections.emptyList(); }
public List<RodBinding<VariantContext>> getResourceRodBindings() { return Collections.emptyList(); }
public boolean alwaysAppendDbsnpId() { return false; }

8
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -142,6 +142,14 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
executeTest("test SLOD", spec);
}
@Test
public void testCompTrack() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
Arrays.asList("71251d8893649ea9abd5d9aa65739ba1"));
executeTest("test using comp track", spec);
}
@Test
public void testOutputParameter() {
HashMap<String, String> e = new HashMap<String, String>();