Package org.monarchinitiative.lirical.core.model

Interface LiricalVariant

All Superinterfaces:

FunctionalAnnotationAware, GenotypedVariant, VariantMetadata

public interface LiricalVariant
extends GenotypedVariant, VariantMetadata, FunctionalAnnotationAware

Method Summary

Modifier and Type	Method	Description
static LiricalVariant	of(GenotypedVariant variant, List<TranscriptAnnotation> annotations, VariantMetadata metadata)
default int	pathogenicClinVarAlleleCount(String sampleId)	Count the number of ClinVar-pathogenic alleles.

Methods inherited from interface org.monarchinitiative.lirical.core.model.FunctionalAnnotationAware

annotations

Methods inherited from interface org.monarchinitiative.lirical.core.model.GenotypedVariant

alleleCount, failedFilters, genomeBuild, passedFilters, sampleNames, variant

Methods inherited from interface org.monarchinitiative.lirical.core.model.VariantMetadata

clinVarAlleleData, clinvarClnSig, frequency, frequencyScore, pathogenicity, pathogenicityScore

Method Details

of

static LiricalVariant of(GenotypedVariant variant,
 List<TranscriptAnnotation> annotations,
 VariantMetadata metadata)

pathogenicClinVarAlleleCount

default int pathogenicClinVarAlleleCount(String sampleId)

Count the number of ClinVar-pathogenic alleles. If this variant is not called Pathogenic in ClinVar, then the count is always zero. If the variant is ClinVar-pathogenic, then the count depends on variant genotype. Homozygous is 2, heterozygous is 1, homozygous reference and not observed are 0.

Returns:

number of pathogenic alleles that are registered in ClinVar