gnomAD MCP Server

Instructions

Implementation Reference

• src/index.ts:732-737 (handler)

  Handler logic for the get_mitochondrial_variants tool. It parses the dataset ID, makes a GraphQL request using the predefined mitochondrial variants query, and formats the result.

  case "get_mitochondrial_variants":
    result = await makeGraphQLRequest(QUERIES.getMitochondrialVariants, {
      datasetId: parseDatasetId((args.dataset as string) || "gnomad_r3"),
    });
    formattedResult = result.data?.mitochondrial_variants || [];
    break;

• src/index.ts:617-630 (registration)

  Tool registration in the ListTools response, defining the name, description, and input schema for get_mitochondrial_variants.

  {
    name: "get_mitochondrial_variants",
    description: "Get mitochondrial variants",
    inputSchema: {
      type: "object",
      properties: {
        dataset: {
          type: "string",
          description: "Dataset ID",
          default: "gnomad_r3",
        },
      },
    },
  },

• src/index.ts:341-358 (schema)

  GraphQL query schema definition for retrieving mitochondrial variants, referenced as QUERIES.getMitochondrialVariants in the handler.

  getMitochondrialVariants: `
    query GetMitochondrialVariants($datasetId: DatasetId!) {
      mitochondrial_variants(dataset: $datasetId) {
        variant_id
        pos
        ref
        alt
        rsids
        ac_het
        ac_hom
        an
        af_het
        af_hom
        max_heteroplasmy
        filters
      }
    }
  `,

• src/index.ts:384-400 (helper)

  Helper function to parse and validate the dataset ID, used in the handler for get_mitochondrial_variants.

  function parseDatasetId(dataset: string): string {
    const validDatasets = [
      "gnomad_r2_1",
      "gnomad_r3",
      "gnomad_r4",
      "gnomad_sv_r2_1",
      "gnomad_sv_r4",
      "gnomad_cnv_r4",
      "exac",
    ];
    
    const datasetLower = dataset.toLowerCase();
    if (!validDatasets.includes(datasetLower)) {
      return "gnomad_r4"; // Default to latest version
    }
    return datasetLower;
  }