gnomad-caf-source.yaml

$schema: "https://json-schema.org/draft/2020-12/schema"
$id: "https://w3id.org/ga4gh/schema/gk-pilot/1.x/gnomad/gnomad-caf-source.yaml"
title: gnomAD Cohort Allele Frequency Study Result profile
type: object

imports:
  va.caf-profile: ../profiles/caf-study-result-source.yaml

$defs:
  GnomadCafProperties:
    description: Additional properties specific to the gnomAD CAF model.
    protectedClassOf: GnomadCAF
    type: object
    maturity: draft
    properties:
      ancillaryResults:
        $ref: "#/$defs/GnomadAncillaryResults"
      qualityMeasures:
        $ref: "#/$defs/GnomadQualityMeasures"
    additionalProperties: true

  GnomadAncillaryResults:
    maturity: draft
    type: object  
    protectedClassOf: GnomadCAF
    description: >-
      Ancillary gnomAD results that may be associated with the CohortAlleleFrequency,
      providing additional context or information.
    properties:
      grpMaxFAF95:
        $ref: "#/$defs/GrpMaxFAF95"
      jointGrpMaxFAF95:
        description: >-
          The Group Max Filtering Allele Frequency (95% confidence interval)
          calculated jointly from genome and exome data.
        $ref: "#/$defs/GrpMaxFAF95"
      homozygotes:
        type: integer
      hemizygotes:
        type: integer
    additionalProperties: false

  GrpMaxFAF95:
    description: The group maximum filtering allele frequency at 95% CI.
    protectedClassOf: GnomadCAF
    type: object
    maturity: draft
    properties:
      frequency:
        type: number
      confidenceInterval:
        type: number
        const: 0.95
        default: 0.95
      groupId:
        type: string
        description: >-
          The genetic ancestry group from which the max frequency was calculated.
    required: [ frequency, confidenceInterval, groupId ]
    additionalProperties: false

  GnomadQualityMeasures:
    maturity: draft
    type: object
    protectedClassOf: GnomadCAF
    description: >-
      Quality measures associated with the gnomAD CohortAlleleFrequency and how it was
      derived, which may impact interpretation.
    properties:
      meanDepth:
        description: >-
          The mean depth of coverage.
        type: number
      fractionCoverage20x:
        description: >-
          The fraction of individuals with at least 20x coverage.
        type: number
      qcFilters:
        type: array
        items:
          type: string
        ordered: false
      monoallelic:
        description: >-
          All samples are homozygous alternate for the variant.
        type: boolean
      lowComplexityRegion:
        description: >-
          This flag indicates the variant is found in a low complexity 
          region. These regions were identified with the symmetric DUST
          algorithm at a score threshold of 30.
        type: boolean
      lowConfidenceLossOfFunctionError:
        description: >-
          Low confidence in predicted Loss of Function (pLoF), where 
          variant is determined by LOFTEE to be unlikely loss of function
          for a transcript.
        type: boolean
      lossOfFunctionWarning:
        description: >-
          A warning provided by LOFTEE to use caution when interpreting 
          the transcript or variant.
        type: boolean
      noncodingTranscriptError:
        description: >-
          Marked in a putative loss of function category by VEP 
          (essential splice, stop-gained, or frameshift) but appears
          on a non-protein-coding transcript.
        type: boolean
      heterozygousSkewedAlleleCount:
        description: >-
          The count of individuals called as heterozygous for this variant 
          with a skewed allele balance, indicating some of these individuals 
          may be miscalled homozygous alternative allele.
        type: integer
    additionalProperties: false

  GnomadCAF:
    maturity: draft
    description: >
      The GA4GH Cohort Allele Frequency Study Result profile, with additional properties
      specific to the gnomAD resource.
    allOf:
      - $ref: "/ga4gh/schema/va-spec/1.x/profiles/json/CohortAlleleFrequencyStudyResult"
      - $ref: "#/$defs/GnomadCafProperties"