render_qc_report
Generate a Markdown QC report for one PGS score or an entire run, summarizing match metrics, chromosome coverage, and per-score details to flag variant-matching issues.
Instructions
Build a Markdown match QC report for one score or a whole run.
A single score gets a focused report; several scores get a run overview, distributions, chromosome coverage, a table of every score and detail sections. For large runs, pass output_path to write the report to disk rather than returning it.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| pgs_ids | No | Optional PGS IDs (e.g. PGS000004) or full accessions to report on. Omit for every score in the file. | |
| log_path | No | Optional path to the variant-level match log, e.g. `{sampleset}_log.csv.gz`. Enables weight, chromosome, indel and match-type metrics. The first read of a large log takes about a minute per few GB; it is then cached. | |
| output_path | No | Optional .md path to write the report to instead of returning it. | |
| summary_path | Yes | Path to the pgsc_calc match summary, e.g. `{sampleset}_summary.csv`. | |
| interpretation | No | Optional Markdown interpretation to place at the top of the report, written after reading the assess_match_qc output and the interpretation guide. It is placed under an Interpretation heading; a leading heading of your own with that name is merged into it. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |