get_region_variants
Retrieve genetic variants from gnomAD database for a specified genomic region using chromosome, start, and stop positions to analyze population genetics data.
Instructions
Get variants in a specific genomic region
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| chrom | Yes | Chromosome (1-22, X, Y) | |
| start | Yes | Start position | |
| stop | Yes | Stop position | |
| dataset | No | Dataset ID | gnomad_r4 |
| reference_genome | No | Reference genome | GRCh38 |
Implementation Reference
- src/index.ts:697-706 (handler)Handler logic for the get_region_variants tool: parses arguments, calls GraphQL query via makeGraphQLRequest, and returns the variants array as JSON.
case "get_region_variants": result = await makeGraphQLRequest(QUERIES.getRegionVariants, { chrom: String(args.chrom), start: parseInt(String(args.start)), stop: parseInt(String(args.stop)), datasetId: parseDatasetId((args.dataset as string) || "gnomad_r4"), referenceGenome: parseReferenceGenome((args.reference_genome as string) || "GRCh38"), }); formattedResult = result.data?.region?.variants || []; break; - src/index.ts:254-280 (schema)GraphQL query schema defining the structure and inputs for fetching region variants from gnomAD API.
getRegionVariants: ` query GetRegionVariants($chrom: String!, $start: Int!, $stop: Int!, $datasetId: DatasetId!, $referenceGenome: ReferenceGenomeId!) { region(chrom: $chrom, start: $start, stop: $stop, reference_genome: $referenceGenome) { variants(dataset: $datasetId) { variant_id pos rsids consequence hgvsc hgvsp lof exome { ac an af filters } genome { ac an af filters } } } } `, - src/index.ts:526-557 (registration)MCP tool registration including name, description, and input schema for get_region_variants.
{ name: "get_region_variants", description: "Get variants in a specific genomic region", inputSchema: { type: "object", properties: { chrom: { type: "string", description: "Chromosome (1-22, X, Y)", }, start: { type: "number", description: "Start position", }, stop: { type: "number", description: "Stop position", }, dataset: { type: "string", description: "Dataset ID", default: "gnomad_r4", }, reference_genome: { type: "string", description: "Reference genome", default: "GRCh38", }, }, required: ["chrom", "start", "stop"], }, }, - src/index.ts:44-61 (helper)Helper function used by all tool handlers, including get_region_variants, to execute GraphQL requests to gnomAD API.
async function makeGraphQLRequest(query: string, variables: Record<string, any> = {}): Promise<GnomadResponse> { const response: Response = await fetch(GNOMAD_API_URL, { method: "POST", headers: { "Content-Type": "application/json", }, body: JSON.stringify({ query, variables, }), }); if (!response.ok) { throw new Error(`HTTP error! status: ${response.status}`); } return await response.json() as GnomadResponse; } - src/index.ts:384-400 (helper)Helper function to validate and parse the dataset ID used in the get_region_variants handler.
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; }