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Genotype quality calculation modified to handle all genotypes the same way. This is inconsistent with GQ output by the UG but is correct even for cases of poor quality genotypes.

This commit is contained in:
Laurent Francioli 2011-10-24 10:24:41 +02:00
parent edea90786a
commit 01b16abc8d
1 changed files with 5 additions and 11 deletions
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16
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
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@ -111,8 +111,8 @@ public class GenotypeLikelihoods {
return likelihoodsMap;
}
//Return the log10 Genotype Quality (GQ) for the given genotype
public double getLog10GQ(Genotype.Type genotype){
//Return the neg log10 Genotype Quality (GQ) for the given genotype
public double getNegLog10GQ(Genotype.Type genotype){
double qual = Double.NEGATIVE_INFINITY;
EnumMap<Genotype.Type,Double> likelihoods = getAsMap(false);
@ -124,15 +124,9 @@ public class GenotypeLikelihoods {
}
qual = likelihoods.get(genotype) - qual;
if (qual < 0) {
// QUAL can be negative if the chosen genotype is not the most likely one individually.
// In this case, we compute the actual genotype probability and QUAL is the likelihood of it not being the chosen one
double[] normalized = MathUtils.normalizeFromLog10(getAsVector());
double chosenGenotype = normalized[genotype.ordinal()-1];
qual = -1.0 * Math.log10(1.0 - chosenGenotype);
}
double[] normalized = MathUtils.normalizeFromLog10(getAsVector());
double chosenGenotype = normalized[genotype.ordinal()-1];
qual = -1.0 * Math.log10(1.0 - chosenGenotype);
return qual;
}