ukb-topmed-phewas-skill

Provide one variant identifier as JSON on stdin, such as {"rsid":"rs7903146"} or {"grch38":"10:112998590-C-T"}, and the script queries the UKB-TOPMed PheWeb API. It returns a bounded list of phenotype associations with total counts and a variant URL.

Pass the GRCh37 coordinate under the grch37 key, for example {"grch37":"10:114758349-C-T"}. The script uses Ensembl GRCh37 and GRCh38 REST endpoints to resolve the position to an rsID and then to the canonical GRCh38 variant before querying UKB-TOPMed.

It accepts exactly one of rsid, grch37, grch38, or variant as a JSON object, or a plain JSON string treated as GRCh38. Variant strings use flexible separators like 10:112998590-C-T or 10-112998590-C-T.

Yes, set save_raw to true and optionally provide raw_output_path. The full JSON response is written to that file (or a default path under /tmp), and the output reports raw_output_path instead of pasting large arrays into chat.

A not_found error occurs when no rsID exists at the given chromosome and position in the Ensembl overlap endpoint for that build. Verify the coordinate and build are correct, or try querying by rsID directly.