get_coverage
Retrieve genomic coverage data for genes from gnomAD to analyze sequencing depth and variant detection reliability in population genetics studies.
Instructions
Get coverage information for a gene
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| gene_id | No | Ensembl gene ID | |
| gene_symbol | No | Gene symbol | |
| dataset | No | Dataset ID | gnomad_r4 |
| reference_genome | No | Reference genome | GRCh38 |
Implementation Reference
- src/index.ts:708-719 (handler)Handler logic for the 'get_coverage' tool within the CallToolRequestSchema handler's switch statement. It validates input, makes a GraphQL request to fetch coverage data, and formats the result.
case "get_coverage": if (!args.gene_id && !args.gene_symbol) { throw new Error("Either gene_id or gene_symbol must be provided"); } result = await makeGraphQLRequest(QUERIES.getCoverage, { geneId: (args.gene_id as string) || null, geneSymbol: (args.gene_symbol as string) || null, datasetId: parseDatasetId((args.dataset as string) || "gnomad_r4"), referenceGenome: parseReferenceGenome((args.reference_genome as string) || "GRCh38"), }); formattedResult = result.data?.gene?.coverage || null; break; - src/index.ts:558-584 (registration)Registration of the 'get_coverage' tool in the ListToolsRequestSchema handler, including name, description, and input schema.
{ name: "get_coverage", description: "Get coverage information for a gene", inputSchema: { type: "object", properties: { gene_id: { type: "string", description: "Ensembl gene ID", }, gene_symbol: { type: "string", description: "Gene symbol", }, dataset: { type: "string", description: "Dataset ID", default: "gnomad_r4", }, reference_genome: { type: "string", description: "Reference genome", default: "GRCh38", }, }, }, }, - src/index.ts:282-317 (schema)GraphQL query schema for fetching gene coverage data, defined in the QUERIES object and used by the handler.
getCoverage: ` query GetCoverage($geneId: String, $geneSymbol: String, $datasetId: DatasetId!, $referenceGenome: ReferenceGenomeId!) { gene(gene_id: $geneId, gene_symbol: $geneSymbol, reference_genome: $referenceGenome) { coverage(dataset: $datasetId) { exome { pos mean median over_1 over_5 over_10 over_15 over_20 over_25 over_30 over_50 over_100 } genome { pos mean median over_1 over_5 over_10 over_15 over_20 over_25 over_30 over_50 over_100 } } } } `, - src/index.ts:44-61 (helper)Helper function used by the get_coverage handler to execute GraphQL requests to the 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; }