variant-linker/schema/variant_annotation.schema.json

CLI for Ensembl VEP and Variant Recoder

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "@context": "https://schema.org",
    "@type": "Dataset",
    "title": "Genetic Variant Annotation Dataset",
    "description": "A dataset generated by Variant-Linker containing variant recoder and VEP annotation data.",
    "type": "object",
    "properties": {
      "meta": {
        "type": "object",
        "properties": {
          "input": { "type": "string" },
          "inputFormat": { "type": "string" },
          "stepsPerformed": {
            "type": "array",
            "items": { "type": "string" }
          },
          "startTime": { "type": "string", "format": "date-time" },
          "endTime": { "type": "string", "format": "date-time" },
          "durationMs": { "type": "number" },
          "recoderCalled": { "type": "boolean" }
        },
        "required": ["input", "inputFormat", "stepsPerformed", "startTime", "endTime", "durationMs", "recoderCalled"]
      },
      "variantData": {
        "oneOf": [
          { "type": "array" },
          { "type": "null" }
        ]
      },
      "annotationData": {
        "type": "array",
        "items": { 
          "type": "object",
          "properties": {
            "deducedInheritancePattern": {
              "type": "object",
              "properties": {
                "patterns": {
                  "type": "array",
                  "items": { "type": "string" },
                  "description": "List of possible inheritance patterns for this variant"
                },
                "confidence": {
                  "type": "string",
                  "enum": ["high", "medium", "low"],
                  "description": "Confidence level in the deduced inheritance pattern"
                },
                "patternDetails": {
                  "type": "object",
                  "description": "Additional details about the inheritance pattern"
                }
              }
            }
          }
        }
      },
      "pedigreeData": {
        "type": "object",
        "description": "Family relationships and affected status from PED file"
      }
    },
    "required": ["meta", "annotationData"]
  }