get_mitochondrial_variants
Retrieve mitochondrial DNA variants from gnomAD to analyze genetic variations in mitochondrial genomes for research and clinical applications.
Instructions
Get mitochondrial variants
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| dataset | No | Dataset ID | gnomad_r3 |
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; }