Variant.yaml

"$schema": https://json-schema.org/draft/2020-12/schema
"$id": https://progenetix.org/services/schemas/Variant/v2020-12-08
title: Variant
meta:
  contributors:
    - description: "GA4GH Data Working Group"
    - description: "Michael Baudis"
      id: "orcid:0000-0002-9903-4248"
  provenance:
    - description: "GA4GH schemas"
      id: 'https://github.com/ga4gh/ga4gh-schemas/blob/master/src/main/proto/ga4gh/variants.proto#L145'
    - description: "Progenetix `bycon` project"
      id: 'https://github.com/progenetix/bycon/'
  used_by:
    - description: "Progenetix database schema (Beacon+ backend)"
      id: 'https://github.com/progenetix/schemas/'
  sb_status: community
description: >
  Genomic variant, representing a sequence variation on a single genomic allele or a structural modification (e.g. copy number variation or LOH). In contrast to the use in e.g. VCF, multi-allelic alterations are reported as single variants.
required:
  all_of:
    - referenceName
      start
  one_of:
    - variantType
      alternateBases
properties:
  id:
    type: string
    description: >
      An internal variant id.
    examples:
      - pgxvar-kftzldsu
  digest:
    type: string
    description: >
      The `digest` patrameter represents a compact concatenation of the essential variant parameters, limited to positional information and either variant type or the combination of reference and alternate bases. Variants which contain a sequence of nucleotides are represented without variant type. The `digest` parameter allows the efficient recovery of "identical" allelic alteration events.
    examples:
      - 11:52900000-134452384:DEL
      - 4:55133558:A>G
  biosampleId:
    type: string
    examples:
      - pgxbs-kftvjtgm
  callsetId:
    type: string
    examples:
      - pgxcs-kftvldsu
  referenceName:
    type: string
    examples:
      - "11"
  mateName:
    type: string
    description: >
      An optional second chromosome, indicating the fusion partner in translocation events.
    examples:
      - X
  referenceBases:
    type: string
    examples:
      - A
      - CGT
  start:
    type: integer
    examples:
      - 52900000
  end:
    type: integer
    examples:
      - 134452384
  alternateBases:
    type: string
    examples:
      - GC
  variantType:
    type: string
    examples:
      - DEL
  externalReferences:
    type: array
    items:
      $ref: OntologyClass.yaml#/properties
    examples:
      - type: Clinvar variant
        id: clinvar:163840
  info:
    type: object
    examples:
      - cnv_value: 3
        var_length: 81552384
  updated:
    type: string
    format: date-time
    examples:
      - "2018-09-26 09:50:51.957159"