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Adding in likelihood calculations for mendelian violations. Also fixing a minor and rare bug in SelectVariants when specifying family structure on the command line.

This commit is contained in:
Christopher Hartl 2011-09-21 16:40:29 -04:00
parent 034b868588
commit 3b51d9106a
3 changed files with 49 additions and 1 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -162,6 +162,12 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
@Argument(fullName="vcfContainsOnlyIndels", shortName="dels",doc="Use if you are annotating an indel vcf, currently VERY experimental", required = false)
protected boolean indelsOnly = false;
@Argument(fullName="family_string",shortName="family",required=false,doc="A family string of the form mom+dad=child for use with the mendelian violation ratio annotation")
public String familyStr = null;
@Argument(fullName="MendelViolationGenotypeQualityThreshold",shortName="mvq",required=false,doc="The genotype quality treshold in order to annotate mendelian violation ratio")
public double minGenotypeQualityP = 0.0;
private VariantAnnotatorEngine engine;
private Collection<VariantContext> indelBufferContext;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -452,7 +452,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
throw new UserException.CouldNotCreateOutputFile(outMVFile, "Can't open output file", e); }
}
else
mvSet.add(new MendelianViolation(getToolkit(), MENDELIAN_VIOLATION_QUAL_THRESHOLD));
mvSet.add(new MendelianViolation(FAMILY_STRUCTURE, MENDELIAN_VIOLATION_QUAL_THRESHOLD));
}
else if (!FAMILY_STRUCTURE.isEmpty()) {
mvSet.add(new MendelianViolation(FAMILY_STRUCTURE, MENDELIAN_VIOLATION_QUAL_THRESHOLD));

42
public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
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@ -1,11 +1,13 @@
package org.broadinstitute.sting.utils;
import org.apache.commons.lang.ArrayUtils;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.datasources.sample.Sample;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import java.util.regex.Matcher;
@ -32,6 +34,9 @@ public class MendelianViolation {
private static Pattern FAMILY_PATTERN = Pattern.compile("(.*)\\+(.*)=(.*)");
static final int[] mvOffsets = new int[] { 1,2,5,6,8,11,15,18,20,21,24,25 };
static final int[] nonMVOffsets = new int[]{ 0,3,4,7,9,10,12,13,14,16,17,19,22,23,26 };
public String getSampleMom() {
return sampleMom;
@ -168,4 +173,41 @@ public class MendelianViolation {
return true;
}
/**
* @return the likelihood ratio for a mendelian violation
*/
public double violationLikelihoodRatio(VariantContext vc) {
double[] logLikAssignments = new double[27];
// the matrix to set up is
// MOM DAD CHILD
// |- AA
// AA AA | AB
// |- BB
// |- AA
// AA AB | AB
// |- BB
// etc. The leaves are counted as 0-11 for MVs and 0-14 for non-MVs
double[] momGL = vc.getGenotype(sampleMom).getLikelihoods().getAsVector();
double[] dadGL = vc.getGenotype(sampleDad).getLikelihoods().getAsVector();
double[] childGL = vc.getGenotype(sampleChild).getLikelihoods().getAsVector();
int offset = 0;
for ( int oMom = 0; oMom < 3; oMom++ ) {
for ( int oDad = 0; oDad < 3; oDad++ ) {
for ( int oChild = 0; oChild < 3; oChild ++ ) {
logLikAssignments[offset++] = momGL[oMom] + dadGL[oDad] + childGL[oChild];
}
}
}
double[] mvLiks = new double[12];
double[] nonMVLiks = new double[15];
for ( int i = 0; i < 12; i ++ ) {
mvLiks[i] = logLikAssignments[mvOffsets[i]];
}
for ( int i = 0; i < 15; i++) {
nonMVLiks[i] = logLikAssignments[nonMVOffsets[i]];
}
return MathUtils.log10sumLog10(mvLiks) - MathUtils.log10sumLog10(nonMVLiks);
}
}