validate_variant_id
Verify variant identifiers and genomic coordinates for accuracy in GTEx genomic data analysis, ensuring valid rs numbers, chromosomes, and positions.
Instructions
Validate variant identifiers and genomic coordinates
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| chr | No | Chromosome (alternative validation method) | |
| position | No | Genomic position (alternative validation method) | |
| variantId | No | Variant ID to validate (rs number or variant ID) |
Implementation Reference
- Core implementation of variant ID validation: queries GTEx API for each variant ID and categorizes as valid/invalid based on presence of data.private async validateVariantIds(variantIds: string[]) { const validVariants: string[] = []; const invalidVariants: string[] = []; // Check each variant ID individually for (const variantId of variantIds) { const result = await this.apiClient.getVariants({ variantId: variantId, datasetId: 'gtex_v8', page: 0, itemsPerPage: 1 }); if (!result.error && result.data && result.data.length > 0) { validVariants.push(variantId); } else { invalidVariants.push(variantId); } } let output = `**Variant ID Validation Results**\n`; output += `Checked: ${variantIds.length} variant IDs\n\n`; if (validVariants.length > 0) { output += `**✅ Valid Variant IDs (${validVariants.length}):**\n`; validVariants.forEach(id => { output += ` • ${id}\n`; }); } if (invalidVariants.length > 0) { output += `\n**❌ Invalid Variant IDs (${invalidVariants.length}):**\n`; invalidVariants.forEach(id => { output += ` • ${id}\n`; }); output += `\n**Note:** Invalid IDs may be due to incorrect format or variants not present in the GTEx dataset.\n`; } return { content: [{ type: "text", text: output }] }; }
- Handler method for validation tools that dispatches to type-specific validators (gene/variant).async validateIds(args: any) { if (!args.ids || !Array.isArray(args.ids) || args.ids.length === 0) { throw new Error('ids parameter is required and must be a non-empty array of IDs to validate'); } const idType = args.type || 'gene'; // 'gene' or 'variant' if (idType === 'gene') { return await this.validateGeneIds(args.ids); } else if (idType === 'variant') { return await this.validateVariantIds(args.ids); } else { throw new Error('type parameter must be either "gene" or "variant"'); } }
- src/index.ts:512-531 (registration)Registration of 'validate_variant_id' tool in ListTools handler, including name, description, and input schema.name: "validate_variant_id", description: "Validate variant identifiers and genomic coordinates", inputSchema: { type: "object", properties: { variantId: { type: "string", description: "Variant ID to validate (rs number or variant ID)" }, chr: { type: "string", description: "Chromosome (alternative validation method)" }, position: { type: "integer", description: "Genomic position (alternative validation method)" } } } },
- src/index.ts:757-762 (handler)Dispatch handler in main CallToolRequestHandler that routes 'validate_variant_id' calls to ReferenceHandlers.validateIds with type 'variant'.if (name === "validate_variant_id") { return await referenceHandlers.validateIds({ ids: [args?.variantId], type: 'variant' }); }