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Adapted for the new version of MendelianViolation

This commit is contained in:
Laurent Francioli 2011-11-30 14:46:38 +01:00
parent 1cb5e9e149
commit 20bffe0430
1 changed files with 23 additions and 34 deletions
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57
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
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@ -12,10 +12,8 @@ import org.broadinstitute.sting.utils.MendelianViolation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.FileNotFoundException;
import java.util.*; import java.util.*;
/** /**
@ -26,42 +24,33 @@ import java.util.*;
public class TransmissionDisequilibriumTest extends InfoFieldAnnotation implements ExperimentalAnnotation { public class TransmissionDisequilibriumTest extends InfoFieldAnnotation implements ExperimentalAnnotation {
private Set<MendelianViolation> fullMVSet = null; private Set<Sample> trios = null;
private final static int REF = 0; private final static int REF = 0;
private final static int HET = 1; private final static int HET = 1;
private final static int HOM = 2; private final static int HOM = 2;
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 ( fullMVSet == null ) { if ( trios == null ) {
fullMVSet = new HashSet<MendelianViolation>();
if ( walker instanceof VariantAnnotator ) { if ( walker instanceof VariantAnnotator ) {
final Map<String,Set<Sample>> families = ((VariantAnnotator) walker).getSampleDB().getFamilies(); trios = ((VariantAnnotator) walker).getSampleDB().getChildrenWithParents();
for( final Set<Sample> family : families.values() ) {
for( final Sample sample : family ) {
if( sample.getParents().size() == 2 && family.containsAll(sample.getParents()) ) { // only works with trios for now
fullMVSet.add( new MendelianViolation(sample, 0.0) );
}
}
}
} else { } else {
throw new UserException("Transmission disequilibrium test annotation can only be used from the Variant Annotator and requires a valid ped file be passed in."); throw new UserException("Transmission disequilibrium test annotation can only be used from the Variant Annotator and requires a valid ped file be passed in.");
} }
} }
final Map<String,Object> toRet = new HashMap<String,Object>(1); final Map<String,Object> toRet = new HashMap<String,Object>(1);
final HashSet<MendelianViolation> mvsToTest = new HashSet<MendelianViolation>(); final HashSet<Sample> triosToTest = new HashSet<Sample>();
for( final MendelianViolation mv : fullMVSet ) { for( final Sample child : trios) {
final boolean hasAppropriateGenotypes = vc.hasGenotype(mv.getSampleChild()) && vc.getGenotype(mv.getSampleChild()).hasLikelihoods() && final boolean hasAppropriateGenotypes = vc.hasGenotype(child.getID()) && vc.getGenotype(child.getID()).hasLikelihoods() &&
vc.hasGenotype(mv.getSampleDad()) && vc.getGenotype(mv.getSampleDad()).hasLikelihoods() && vc.hasGenotype(child.getPaternalID()) && vc.getGenotype(child.getPaternalID()).hasLikelihoods() &&
vc.hasGenotype(mv.getSampleMom()) && vc.getGenotype(mv.getSampleMom()).hasLikelihoods(); vc.hasGenotype(child.getMaternalID()) && vc.getGenotype(child.getMaternalID()).hasLikelihoods();
if ( hasAppropriateGenotypes ) { if ( hasAppropriateGenotypes ) {
mvsToTest.add(mv); triosToTest.add(child);
} }
} }
toRet.put("TDT", calculateTDT( vc, mvsToTest )); toRet.put("TDT", calculateTDT( vc, triosToTest ));
return toRet; return toRet;
} }
@ -72,27 +61,27 @@ public class TransmissionDisequilibriumTest extends InfoFieldAnnotation implemen
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("TDT", 1, VCFHeaderLineType.Float, "Test statistic from Wittkowski transmission disequilibrium test.")); } public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("TDT", 1, VCFHeaderLineType.Float, "Test statistic from Wittkowski transmission disequilibrium test.")); }
// Following derivation in http://en.wikipedia.org/wiki/Transmission_disequilibrium_test#A_modified_version_of_the_TDT // Following derivation in http://en.wikipedia.org/wiki/Transmission_disequilibrium_test#A_modified_version_of_the_TDT
private double calculateTDT( final VariantContext vc, final Set<MendelianViolation> mvsToTest ) { private double calculateTDT( final VariantContext vc, final Set<Sample> triosToTest ) {
final double nABGivenABandBB = calculateNChildren(vc, mvsToTest, HET, HET, HOM); final double nABGivenABandBB = calculateNChildren(vc, triosToTest, HET, HET, HOM);
final double nBBGivenABandBB = calculateNChildren(vc, mvsToTest, HOM, HET, HOM); final double nBBGivenABandBB = calculateNChildren(vc, triosToTest, HOM, HET, HOM);
final double nAAGivenABandAB = calculateNChildren(vc, mvsToTest, REF, HET, HET); final double nAAGivenABandAB = calculateNChildren(vc, triosToTest, REF, HET, HET);
final double nBBGivenABandAB = calculateNChildren(vc, mvsToTest, HOM, HET, HET); final double nBBGivenABandAB = calculateNChildren(vc, triosToTest, HOM, HET, HET);
final double nAAGivenAAandAB = calculateNChildren(vc, mvsToTest, REF, REF, HET); final double nAAGivenAAandAB = calculateNChildren(vc, triosToTest, REF, REF, HET);
final double nABGivenAAandAB = calculateNChildren(vc, mvsToTest, HET, REF, HET); final double nABGivenAAandAB = calculateNChildren(vc, triosToTest, HET, REF, HET);
final double numer = (nABGivenABandBB - nBBGivenABandBB) + 2.0 * (nAAGivenABandAB - nBBGivenABandAB) + (nAAGivenAAandAB - nABGivenAAandAB); final double numer = (nABGivenABandBB - nBBGivenABandBB) + 2.0 * (nAAGivenABandAB - nBBGivenABandAB) + (nAAGivenAAandAB - nABGivenAAandAB);
final double denom = (nABGivenABandBB + nBBGivenABandBB) + 4.0 * (nAAGivenABandAB + nBBGivenABandAB) + (nAAGivenAAandAB + nABGivenAAandAB); final double denom = (nABGivenABandBB + nBBGivenABandBB) + 4.0 * (nAAGivenABandAB + nBBGivenABandAB) + (nAAGivenAAandAB + nABGivenAAandAB);
return (numer * numer) / denom; return (numer * numer) / denom;
} }
private double calculateNChildren( final VariantContext vc, final Set<MendelianViolation> mvsToTest, final int childIdx, final int momIdx, final int dadIdx ) { private double calculateNChildren( final VariantContext vc, final Set<Sample> triosToTest, final int childIdx, final int momIdx, final int dadIdx ) {
final double likelihoodVector[] = new double[mvsToTest.size() * 2]; final double likelihoodVector[] = new double[triosToTest.size() * 2];
int iii = 0; int iii = 0;
for( final MendelianViolation mv : mvsToTest ) { for( final Sample child : triosToTest ) {
final double[] momGL = vc.getGenotype(mv.getSampleMom()).getLikelihoods().getAsVector(); final double[] momGL = vc.getGenotype(child.getMaternalID()).getLikelihoods().getAsVector();
final double[] dadGL = vc.getGenotype(mv.getSampleDad()).getLikelihoods().getAsVector(); final double[] dadGL = vc.getGenotype(child.getPaternalID()).getLikelihoods().getAsVector();
final double[] childGL = vc.getGenotype(mv.getSampleChild()).getLikelihoods().getAsVector(); final double[] childGL = vc.getGenotype(child.getID()).getLikelihoods().getAsVector();
likelihoodVector[iii++] = momGL[momIdx] + dadGL[dadIdx] + childGL[childIdx]; likelihoodVector[iii++] = momGL[momIdx] + dadGL[dadIdx] + childGL[childIdx];
likelihoodVector[iii++] = momGL[dadIdx] + dadGL[momIdx] + childGL[childIdx]; likelihoodVector[iii++] = momGL[dadIdx] + dadGL[momIdx] + childGL[childIdx];
} }