biobankjapan-phewas-skill

Provide one variant identifier as JSON on stdin, such as {"rsid":"rs7903146"} or {"grch37":"10:114758349-C-T"}, and the script queries the pheweb.jp API. It returns a JSON summary with association counts, truncated results, and a variant URL.

It accepts exactly one of rsid, grch37, grch38, or variant keys, with coordinates in chrom-pos-ref-alt form using flexible separators. GRCh38 and rsID inputs are resolved to GRCh37 through Ensembl before querying BioBank Japan.

Yes, the script resolves GRCh38 input by finding the overlapping rsID via the Ensembl overlap endpoint, then looking up its GRCh37 mapping. If resolution fails, it returns an error with code resolution_failed or not_found.

Set save_raw to true in the input JSON, optionally with raw_output_path, and the full API payload is written to disk. The response reports raw_output_path so you can inspect the complete data without large chat output.

The not_found error occurs when no rsID exists at the given position in the Ensembl overlap endpoint for that build. A 404 from BioBank Japan instead returns ok=true with zero associations and a warning that the variant is absent from the PheWAS API.