get_variant_liftover
Convert genomic variant coordinates between GRCh37 and GRCh38 reference genomes using the gnomAD database, enabling cross-version data analysis and comparison.
Instructions
[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.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| reference_genome | Yes | ||
| source_variant_id | No | ||
| liftover_variant_id | No | ||
| dataset | No | gnomad_r2_1 |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
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)