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PED support for Inbreeding Coefficient annotation 

Signed-off-by: Eric Banks <ebanks@broadinstitute.org>
This commit is contained in:
Laurent Francioli 2012-04-25 16:51:16 +02:00 committed by Eric Banks
parent c2b74eca64
commit 96e5a26223
2 changed files with 17 additions and 5 deletions
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12
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
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@ -4,6 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
@ -16,10 +17,7 @@ import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypesContext; import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.Arrays; import java.util.*;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/** /**
@ -33,8 +31,12 @@ import java.util.Map;
public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
private static final int MIN_SAMPLES = 10; private static final int MIN_SAMPLES = 10;
private Set<String> founderIds;
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) { public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
//If available, get the founder IDs and cache them. the IC will only be computed on founders then.
if(founderIds == null)
founderIds = ((Walker)walker).getSampleDB().getFounderIds();
return calculateIC(vc); return calculateIC(vc);
} }
@ -43,7 +45,7 @@ public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnno
} }
private Map<String, Object> calculateIC(final VariantContext vc) { private Map<String, Object> calculateIC(final VariantContext vc) {
final GenotypesContext genotypes = vc.getGenotypes(); final GenotypesContext genotypes = (founderIds == null || founderIds.isEmpty()) ? vc.getGenotypes() : vc.getGenotypes(founderIds);
if ( genotypes == null || genotypes.size() < MIN_SAMPLES ) if ( genotypes == null || genotypes.size() < MIN_SAMPLES )
return null; return null;

10
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -198,4 +198,14 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
executeTest("Testing ChromosomeCounts annotation with PED file", spec); executeTest("Testing ChromosomeCounts annotation with PED file", spec);
} }
@Test
public void testInbreedingCoeffPed() {
final String MD5 = "7f1314fada5cb1f35ba1996f8a7a686b";
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf" +
" -L " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf -NO_HEADER -ped " + validationDataLocation + "ug.random50000.family.ped -o %s", 1,
Arrays.asList(MD5));
executeTest("Testing InbreedingCoeff annotation with PED file", spec);
}
} }