private Genotype CalculateHaploidGenotype(IEnumerable <CalledAllele> alleles,
int minDepthToGenotype, out List <CalledAllele> allelesToPrune)
{
allelesToPrune = new List <CalledAllele>();
var singleGTForLoci = Genotype.HemizygousNoCall;
var orderedVariants = GenotypeCalculatorUtilities.FilterAndOrderAllelesByFrequency(alleles, allelesToPrune, _minorVF);
var referenceFrequency = GenotypeCalculatorUtilities.GetReferenceFrequency(alleles, _minorVF);
var refExists = (referenceFrequency >= _minorVF);
var depthIssue = GenotypeCalculatorUtilities.CheckForDepthIssue(alleles, minDepthToGenotype);
bool refCall = ((orderedVariants.Count == 0) || (orderedVariants[0].Frequency < _minorVF));
if (!depthIssue && refCall && refExists && referenceFrequency > _majorVF)
{
singleGTForLoci = Genotype.HemizygousRef;
}
if (!depthIssue && !refCall && !refExists && orderedVariants[0].Frequency > _majorVF)
{
singleGTForLoci = Genotype.HemizygousAlt;
}
//if (!diploidModelFail)
allelesToPrune = GenotypeCalculatorUtilities.GetAllelesToPruneBasedOnGTCall(singleGTForLoci, orderedVariants, allelesToPrune);
return(singleGTForLoci);
}
private static Genotype CalculateDiploidGenotype(IEnumerable <CalledAllele> alleles,
int minDepthToGenotype, DiploidThresholdingParameters snvThresholdingParameters,
DiploidThresholdingParameters indelThresholdingParameters, out List <CalledAllele> allelesToPrune)
{
allelesToPrune = new List <CalledAllele>();
var orderedVariants = GenotypeCalculatorUtilities.FilterAndOrderAllelesByFrequency(alleles, allelesToPrune, snvThresholdingParameters.MinorVF);
var referenceFrequency = GenotypeCalculatorUtilities.GetReferenceFrequency(alleles, snvThresholdingParameters.MinorVF);
var refExists = (referenceFrequency >= snvThresholdingParameters.MinorVF);
var depthIssue = GenotypeCalculatorUtilities.CheckForDepthIssue(alleles, minDepthToGenotype);
var parameters = snvThresholdingParameters;
bool refCall = orderedVariants.Count == 0 || (orderedVariants[0].Frequency < snvThresholdingParameters.MinorVF);
//do we apply SNP threshholds or indel thresholds?
parameters = SelectParameters(indelThresholdingParameters, orderedVariants, parameters, refCall);
var preliminaryGenotype = GetPreliminaryGenotype(orderedVariants, parameters, refCall);
var finalGTForLoci = GenotypeCalculatorUtilities.ConvertSimpleGenotypeToComplexGenotype(alleles, orderedVariants, referenceFrequency, refExists, depthIssue, refCall,
parameters.MinorVF, parameters.SumVFforMultiAllelicSite, preliminaryGenotype);
allelesToPrune = GenotypeCalculatorUtilities.GetAllelesToPruneBasedOnGTCall(finalGTForLoci, orderedVariants, allelesToPrune);
return(finalGTForLoci);
}
private static Genotype CalculateDiploidGenotypeFromBinomialModel(
IEnumerable <CalledAllele> alleles,
int minDepthToGenotype,
AdaptiveGenotypingParameters adaptiveGenotypingParameters,
out List <CalledAllele> allelesToPrune)
{
allelesToPrune = new List <CalledAllele>();
float minVariantFrequency = GetMinVarFrequency(alleles.First().TotalCoverage,
adaptiveGenotypingParameters.SnvModel, adaptiveGenotypingParameters.SnvPrior);
double referenceFrequency = GetReferenceFrequency(alleles);
bool depthIssue = GenotypeCalculatorUtilities.CheckForDepthIssue(alleles, minDepthToGenotype);
bool refExists = referenceFrequency > minVariantFrequency;
List <CalledAllele> orderedVariants = GenotypeCalculatorUtilities.FilterAndOrderAllelesByFrequency(alleles,
allelesToPrune, minVariantFrequency);
bool refCall = orderedVariants.Count == 0;
//assume its ref call
var preliminaryGenotype = SimplifiedDiploidGenotype.HomozygousRef;
//this is order by descending - so most frequent is first.
if (!refCall)
{
//do we apply SNP threshholds or indel thresholds?
var dominantVariant = orderedVariants[0];
var(model, priors) = adaptiveGenotypingParameters.GetModelsAndPriors(dominantVariant);
preliminaryGenotype = AdaptiveGenotyperCalculator.GetSimplifiedGenotype(dominantVariant, model, priors);
minVariantFrequency = GetMinVarFrequency(dominantVariant.TotalCoverage, model, priors);
}
var finalGTForLoci = GenotypeCalculatorUtilities.ConvertSimpleGenotypeToComplexGenotype(alleles, orderedVariants,
referenceFrequency, refExists, depthIssue, refCall, minVariantFrequency,
adaptiveGenotypingParameters.SumVFforMultiAllelicSite, preliminaryGenotype);
allelesToPrune = GenotypeCalculatorUtilities.GetAllelesToPruneBasedOnGTCall(finalGTForLoci, orderedVariants, allelesToPrune);
return(finalGTForLoci);
}
