get_structural_variants

Retrieve structural variant data from gnomAD for a specific genomic region to analyze chromosomal rearrangements, deletions, duplications, and inversions.

Instructions

Get structural variants in a genomic region

Input Schema

TableJSON Schema

Name	Required	Description	Default
`chrom`	Yes	Chromosome
`start`	Yes	Start position
`stop`	Yes	Stop position
`dataset`	No	Dataset ID (gnomad_sv_r4, gnomad_sv_r2_1)	gnomad_sv_r4
`reference_genome`	No	Reference genome	GRCh38

Implementation Reference

src/index.ts:721-730 (handler)

The main handler logic for the get_structural_variants tool within the CallToolRequestHandler switch statement. It parses arguments, calls makeGraphQLRequest with the appropriate query and variables, and extracts the structural_variants from the response data.

case "get_structural_variants":
  result = await makeGraphQLRequest(QUERIES.getStructuralVariants, {
    chrom: String(args.chrom),
    start: parseInt(String(args.start)),
    stop: parseInt(String(args.stop)),
    datasetId: parseDatasetId((args.dataset as string) || "gnomad_sv_r4"),
    referenceGenome: parseReferenceGenome((args.reference_genome as string) || "GRCh38"),
  });
  formattedResult = result.data?.region?.structural_variants || [];
  break;

src/index.ts:585-616 (registration)

Registration of the 'get_structural_variants' tool in the ListToolsRequestHandler response, defining its name, description, and input schema.

{
  name: "get_structural_variants",
  description: "Get structural variants in a genomic region",
  inputSchema: {
    type: "object",
    properties: {
      chrom: {
        type: "string",
        description: "Chromosome",
      },
      start: {
        type: "number",
        description: "Start position",
      },
      stop: {
        type: "number",
        description: "Stop position",
      },
      dataset: {
        type: "string",
        description: "Dataset ID (gnomad_sv_r4, gnomad_sv_r2_1)",
        default: "gnomad_sv_r4",
      },
      reference_genome: {
        type: "string",
        description: "Reference genome",
        default: "GRCh38",
      },
    },
    required: ["chrom", "start", "stop"],
  },
},

src/index.ts:588-615 (schema)

Input schema for the get_structural_variants tool, defining parameters like chrom, start, stop, dataset, and reference_genome with types and requirements.

inputSchema: {
  type: "object",
  properties: {
    chrom: {
      type: "string",
      description: "Chromosome",
    },
    start: {
      type: "number",
      description: "Start position",
    },
    stop: {
      type: "number",
      description: "Stop position",
    },
    dataset: {
      type: "string",
      description: "Dataset ID (gnomad_sv_r4, gnomad_sv_r2_1)",
      default: "gnomad_sv_r4",
    },
    reference_genome: {
      type: "string",
      description: "Reference genome",
      default: "GRCh38",
    },
  },
  required: ["chrom", "start", "stop"],
},

src/index.ts:319-339 (helper)

GraphQL query template (QUERIES.getStructuralVariants) used by the handler to fetch structural variants data from gnomAD API for a given genomic region.

getStructuralVariants: `
  query GetStructuralVariants($chrom: String!, $start: Int!, $stop: Int!, $datasetId: DatasetId!, $referenceGenome: ReferenceGenomeId!) {
    region(chrom: $chrom, start: $start, stop: $stop, reference_genome: $referenceGenome) {
      structural_variants(dataset: $datasetId) {
        variant_id
        chrom
        pos
        end
        length
        type
        alts
        ac
        an
        af
        homozygote_count
        hemizygote_count
        filters
      }
    }
  }
`,

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