public static SimplifiedDiploidGenotype GetSimplifiedGenotype(int alleleDepth, int totalDepth, double[] means,
double[] priors)
{
// Get genotype category
double[] posteriors = CalculatePosteriors(alleleDepth, totalDepth, means, priors);
var maxPosterior = posteriors.Max();
int category = Array.IndexOf(posteriors, maxPosterior);
return(MixtureModelResult.IntToGenotypeCategory(category));
}
public static MixtureModelResult CalculateQScoreAndGenotypePosteriors(int alleleDepth, int totalDepth, double[] means,
double[] priors)
{
// Get genotype category
int category = MixtureModelResult.GenotypeCategoryToInt(GetSimplifiedGenotype(alleleDepth,
totalDepth, means, priors));
// Get Q score and genotype posterior
(int qScore, float[] genotypePosteriors) = CalculateQScoreAndGenotypePosteriors(alleleDepth, totalDepth, category,
means, priors, _defaultQScoreEffectiveN);
return(new MixtureModelResult
{
GenotypeCategoryAsInt = category,
QScore = qScore,
GenotypePosteriors = genotypePosteriors
});
}
public List <CalledAllele> SetGenotypes(IEnumerable <CalledAllele> alleles)
{
var singleGTForLoci = CalculateDiploidGenotypeFromBinomialModel(alleles, MinDepthToGenotype,
_adaptiveGenotypingParameters, out var allelesToPrune);
int phaseSetIndex = 1; //reserve -1 for unset, and 0 for reference, and 1 and 2 for alts
foreach (var allele in alleles)
{
allele.Genotype = singleGTForLoci;
if (allele.TotalCoverage == 0)
{
allele.GenotypeQscore = MinGQScore;
allele.GenotypePosteriors = new float[] {
_adaptiveGenotypingParameters.MaxGenotypePosteriors,
_adaptiveGenotypingParameters.MaxGenotypePosteriors,
_adaptiveGenotypingParameters.MaxGenotypePosteriors
};
}
else
{
var(model, prior) = _adaptiveGenotypingParameters.GetModelsAndPriors(allele);
MixtureModelResult adaptiveGTResult = AdaptiveGenotyperCalculator.GetGenotypeAndQScore(allele,
model, prior);
allele.GenotypeQscore = Math.Max(Math.Min(adaptiveGTResult.QScore, MaxGQScore), MinGQScore);
allele.GenotypePosteriors = adaptiveGTResult.GenotypePosteriors;
}
if (allele.IsRefType)
{
allele.PhaseSetIndex = 0;
}
else
{
allele.PhaseSetIndex = phaseSetIndex;
phaseSetIndex++;
}
}
// Calculate GP for multiallelic variant based on multinomial distribution
if (alleles.First().Genotype == Genotype.HeterozygousAlt1Alt2)
{
CalledAllele allele1 = alleles.First(), allele2 = alleles.ElementAt(1);
var(model1, _) = _adaptiveGenotypingParameters.GetModelsAndPriors(allele1);
var(model2, _) = _adaptiveGenotypingParameters.GetModelsAndPriors(allele2);
var mixtureModelResult = AdaptiveGenotyperCalculator.GetMultiAllelicQScores(allele1, allele2,
new List <double[]> {
model1, model2
});
foreach (CalledAllele allele in alleles)
{
allele.GenotypeQscore = Math.Max(Math.Min(mixtureModelResult.QScore, MaxGQScore), MinGQScore);
allele.GenotypePosteriors = mixtureModelResult.GenotypePosteriors;
}
}
return(allelesToPrune);
}
