gnomAD MCP Server

Instructions

Implementation Reference

• server.py:278-318 (handler)

  The implementation of get_variant_liftover, which validates input parameters and calls run_query_with_metadata to fetch liftover data.

  def get_variant_liftover(
      reference_genome: str,
      source_variant_id: Optional[str] = None,
      liftover_variant_id: Optional[str] = None,
      dataset: str = 'gnomad_r2_1'
  ) -> dict:
      """
      [gnomAD API] Retrieve liftover info (v2 only)
      Args:
          reference_genome (str): Reference genome (GRCh37 or GRCh38)
          source_variant_id (str, optional): Source variant ID (e.g. 12-112241766-G-A on GRCh37)
          liftover_variant_id (str, optional): Lifted over variant ID (e.g. 12-111803962-G-A on GRCh38)
      Returns:
          dict: liftover info
      Note:
          Not supported in v3/v4.
      """
  
      if dataset != 'gnomad_r2_1':
          raise ValueError("Only v2 is supported for liftover.")
      
      if source_variant_id and liftover_variant_id:
          raise ValueError("Only one of source_variant_id or liftover_variant_id must be provided.")
      
      # Build check
      if source_variant_id:
          if reference_genome != 'GRCh37':
              raise ValueError("Source variant ID must be on GRCh37.")
      elif liftover_variant_id:
          if reference_genome != 'GRCh38':
              raise ValueError("Lifted over variant ID must be on GRCh38.")
      else:
          raise ValueError("Either source_variant_id or liftover_variant_id must be provided.")
  
      variables = {
          'dataset': dataset,
          'reference_genome': reference_genome,
          'source_variant_id': source_variant_id,
          'liftover_variant_id': liftover_variant_id,
      }
      return run_query_with_metadata('liftover', variables)