gnomAD MCP Server

Instructions

Implementation Reference

• server.py:199-225 (handler)

  The tool 'get_copy_number_variant_info' is defined in server.py using the @mcp.tool() decorator. It validates the dataset and reference genome parameters before calling 'run_query_with_metadata' to fetch the CNV information from the gnomAD API.

  def get_copy_number_variant_info(
      reference_genome: str,
      variantId: str,
      dataset: str = 'gnomad_cnv_r4'
  ) -> dict:
      """
      [gnomAD API] Retrieve copy number variant info (v4 only)
      Args:
          reference_genome (str): Reference genome (GRCh38)
          variantId (str): CNV ID (e.g. 18714__DUP)
      Returns:
          dict: CNV info
      Note:
          Not supported in v2/v3.
      """
  
      if dataset != 'gnomad_cnv_r4':
          raise ValueError("Only v4 is supported for copy number variant info.")
      if reference_genome != 'GRCh38':
          raise ValueError("Only GRCh38 is supported for copy number variant info.")
  
      variables = {
          'dataset': dataset,
          'reference_genome': reference_genome,
          'variantId': variantId,
      }
      return run_query_with_metadata('copy_number_variant', variables)