gnomAD MCP Server

Instructions

Implementation Reference

• server.py:64-97 (handler)

  The get_region_info tool is defined and implemented as an MCP tool in server.py. It takes region parameters, validates them, and calls run_query_with_metadata to fetch data.

  @mcp.tool()
  def get_region_info(
      reference_genome: str,
      chrom: str,
      start: int,
      stop: int,
      dataset: str = 'gnomad_r4'
  ) -> dict:
      """
      [gnomAD API] Retrieve region information (v4 only)
      Args:
          reference_genome (str): Reference genome (GRCh38)
          chrom (str): Chromosome
          start (int): Start position. Build must be GRCh38.
          stop (int): End position. Build must be GRCh38. 
      Returns:
          dict: region info
      Note:
          Not supported in v2/v3.
      """
  
      if dataset != 'gnomad_r4':
          raise ValueError("Only v4 is supported for region info.")
      if reference_genome != 'GRCh38':
          raise ValueError("Only GRCh38 is supported for region info.")
  
      variables = {
          'dataset': dataset,
          'reference_genome': reference_genome,
          'chrom': chrom,
          'start': start,
          'stop': stop,
      }
      return run_query_with_metadata('region', variables)