private static List <CalledAllele> ProcessMultiAllelicLocus(List <CalledAllele> orderedVariants,
RecalibrationResults results)
{
RecalibrationResult resultForVariant = GetModelFromType(orderedVariants[0], results);
MixtureModelResult mixtureModelResult = GetModelResult(orderedVariants[0], resultForVariant);
switch (mixtureModelResult.GenotypeCategory)
{
case SimplifiedDiploidGenotype.HomozygousRef:
case SimplifiedDiploidGenotype.HomozygousAlt:
var allele = UpdateGenotypeAndQScore(orderedVariants[0], mixtureModelResult);
return(new List <CalledAllele> {
allele
});
case SimplifiedDiploidGenotype.HeterozygousAltRef:
orderedVariants[0].Genotype = Genotype.HeterozygousAlt1Alt2;
orderedVariants[1].Genotype = Genotype.HeterozygousAlt1Alt2;
orderedVariants = UpdateMultiAllelicQScores(orderedVariants, results);
return(orderedVariants);
default:
throw new ArgumentException("Invalid model results");
}
}
private static List <CalledAllele> UpdateMultiAllelicQScores(List <CalledAllele> variantList, RecalibrationResults results)
{
// Determine model types
RecalibrationResult model1 = GetModelFromType(variantList[0], results);
RecalibrationResult model2 = GetModelFromType(variantList[1], results);
// Calculate posteriors based on multinomial distribution
int dp = variantList[0].TotalCoverage;
int[] ad = new int[3];
ad[2] = variantList[0].AlleleSupport; //temp[1];
ad[1] = variantList[1].AlleleSupport; //temp[0];
ad[0] = dp - ad[1] - ad[2];
if (ad[0] < 0)
{
ad[0] = 0;
dp = ad[1] + ad[2];
}
var mixtureModelResult = MixtureModel.GetMultinomialQScores(ad, dp,
new List <double[]> {
model1.Means, model2.Means
});
// Update variant genotypes fields
variantList[0].GenotypePosteriors = mixtureModelResult.GenotypePosteriors;
variantList[1].GenotypePosteriors = mixtureModelResult.GenotypePosteriors;
variantList[0].GenotypeQscore = mixtureModelResult.QScore;
variantList[1].GenotypeQscore = mixtureModelResult.QScore;
return(variantList);
}
private static MixtureModelResult GetModelResult(CalledAllele allele, RecalibrationResult result)
{
var recal = new RecalibratedVariantsCollection();
recal.AddLocus(allele);
return(MixtureModel.UsePrefitModel(recal.Ad, recal.Dp, result.Means, result.Priors).PrimaryResult);
}
private static List <CalledAllele> ProcessSingleVariantLocus(CalledAllele allele,
RecalibrationResults results)
{
RecalibrationResult resultForVariant = GetModelFromType(allele, results);
return(new List <CalledAllele> {
UpdateVariant(allele, resultForVariant)
});
}
private static CalledAllele UpdateVariant(CalledAllele allele, RecalibrationResult result)
{
// Get model results
string key = allele.Chromosome + ":" + allele.ReferencePosition.ToString();
MixtureModelResult mixtureModelResult;
if (result.Variants.ContainsKey(key))
{
mixtureModelResult = result.Variants[key].MixtureModelResult;
}
else
{
mixtureModelResult = GetModelResult(allele, result);
}
return(UpdateGenotypeAndQScore(allele, mixtureModelResult));
}
