gwasharmonizer-mcp

# GWAS Harmoniser MCP An MCP server that lets AI agents harmonize local GWAS summary-statistics files with the strict workflow at [gwasharmonizer.org](https://gwasharmonizer.org/). Use it when a researcher asks to harmonize or harmonise GWAS sumstats, standardize columns, align effect and non-effect alleles, handle GRCh37/GRCh38 liftover, validate rsIDs, run harmonization QC, or prepare summary statistics for meta-analysis, downstream analysis, submission, or a paper. It does not run association tests. ## Install Install via `uv`: ```bash uv tool install gwasharmonizer-mcp ``` Or via `pip`: ```bash pip install gwasharmonizer-mcp ``` ### Register with your AI client **Codex:** ```bash codex mcp add gwasharmonizer -- gwasharmonizer-mcp ``` **Claude Code:** ```bash claude mcp add --transport stdio --scope user gwasharmonizer -- gwasharmonizer-mcp ``` By default, local inputs must be under `~/Desktop`. Files are uploaded to the configured live service for processing; raw variant rows are not returned to the agent through the MCP. ## Agent tools - `start_harmonization`: start harmonization for a local GWAS file. Use `output_profile="strict_meta"` for a full-file `META_READY` METAL export and `download_kind="data"` when only the `.tsv.gz` output should be downloaded. - `get_harmonization`: check progress, required confirmations, blockers, and artifact paths. - `confirm_harmonization`: resume only with scientific metadata the user verified from authoritative study documentation. Example request: `Harmonize ~/Desktop/study.tsv.gz for meta-analysis, verify META_READY, and download only the output file.` See the public [agent and MCP guide](https://gwasharmonizer.org/agents) for routing terms and scientific boundaries. ### Resumable uploads (0.1.2) Uploads use checksum-verified 8 MiB chunks when the backend supports them. Each request has at most three transient attempts. Calling `start_harmonization` again with the same file/options after a transfer failure …