pgs-mcp
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| PGS_MCP_CACHE_DIR | No | Optional directory for aggregated log data cache. Defaults to ~/.cache/pgs-mcp. |
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Features and capabilities supported by this server
Protocol revision2025-11-25
| Capability | Details |
|---|---|
| tools | {
"listChanged": false
} |
| prompts | {
"listChanged": false
} |
| resources | {
"subscribe": false,
"listChanged": false
} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| assess_match_qcA | Assess how well polygenic scores matched a target genotype dataset in pgsc_calc. Works for a single score or a whole run. Returns raw metrics (variant match rate, weight coverage, strand handling, exclusions, per-chromosome coverage), structural warnings and descriptive observations. Large runs return a compact index of every score; request specific pgs_ids for full detail. Interpret with the guide at pgs://guides/match-qc. |
| render_qc_reportA | 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. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
| interpret_match_qc | Assess pgsc_calc match QC and write a guided interpretation of the results. |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
| match-qc-guide | What each match QC metric and warning means, likely causes, and how to write an interpretation for one score or a full run. |
TDQS
Scored across 2 tools
The two tools have mostly distinct roles: assess_match_qc computes metrics and warnings, while render_qc_report produces a Markdown report. A user might still briefly wonder whether to call assessment before rendering, but the descriptions make the boundary clear enough.
Both names use snake_case and begin with a verb, giving a predictable style. The internal ordering differs slightly between assess_match_qc and render_qc_report, but it is not confusing.
Two tools are quite thin for a server surface, even for a specialized QC workflow. The tools are well-scoped, but the server sits at the borderline of feeling under-provisioned.
The surface covers the core workflow of assessing match QC and rendering a report for single scores or whole runs. Minor gaps may exist around discovery or filtering, but the main lifecycle is represented.