{"$schema":"https://wellknown.network/schemas/agent-record-v1.json","schemaVersion":"1","id":"ag_r5g5nr38ursg","handle":"gwasharmonizer-mcp","url":"https://wellknown.network/agents/gwasharmonizer-mcp","links":{"self":"https://wellknown.network/agents/gwasharmonizer-mcp/record.json","html":"https://wellknown.network/agents/gwasharmonizer-mcp","markdown":"https://wellknown.network/agents/gwasharmonizer-mcp/record.md","api":"https://wellknown.network/api/v1/agents/gwasharmonizer-mcp","status":"https://wellknown.network/api/v1/agents/gwasharmonizer-mcp/status","claim":"https://wellknown.network/agents/gwasharmonizer-mcp/claim","claimApi":"https://wellknown.network/api/v1/claims","claimDescriptor":"https://wellknown.network/agents/gwasharmonizer-mcp/claim.json","badge":"https://wellknown.network/agents/gwasharmonizer-mcp/badge.svg","openapi":"https://wellknown.network/openapi.json","history":"https://wellknown.network/api/v1/agents/gwasharmonizer-mcp/history","tools":"https://wellknown.network/api/v1/agents/gwasharmonizer-mcp/tools"},"ard":{"identifier":"urn:air::server:gwasharmonizer-mcp","type":"application/mcp-server-card+json"},"kind":"mcp_server","declared":{"name":"gwasharmonizer-mcp","summary":"MCP server and CLI for agent-driven GWAS summary-statistics harmonization","description":"# GWAS Harmoniser MCP\n\nAn MCP server that lets AI agents harmonize local GWAS summary-statistics files with the strict workflow at [gwasharmonizer.org](https://gwasharmonizer.org/).\n\nUse 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.\n\n## Install\n\nInstall via `uv`:\n\n```bash\nuv tool install gwasharmonizer-mcp\n```\n\nOr via `pip`:\n```bash\npip install gwasharmonizer-mcp\n```\n\n### Register with your AI client\n\n**Codex:**\n```bash\ncodex mcp add gwasharmonizer -- gwasharmonizer-mcp\n```\n\n**Claude Code:**\n```bash\nclaude mcp add --transport stdio --scope user gwasharmonizer -- gwasharmonizer-mcp\n```\n\nBy 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.\n\n## Agent tools\n\n- `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.\n- `get_harmonization`: check progress, required confirmations, blockers, and artifact paths.\n- `confirm_harmonization`: resume only with scientific metadata the user verified from authoritative study documentation.\n\nExample request: `Harmonize ~/Desktop/study.tsv.gz for meta-analysis, verify META_READY, and download only the output file.`\n\nSee the public [agent and MCP guide](https://gwasharmonizer.org/agents) for routing terms and scientific boundaries.\n\n### Resumable uploads (0.1.2)\n\nUploads use checksum-verified 8 MiB chunks when the backend supports them. Each\nrequest has at most three transient attempts. Calling `start_harmonization` again\nwith the same file/options after a transfer failure …","publisher":null,"homepage":"https://gwasharmonizer.org/agents","repository":"https://github.com/MadisLemsalu/gwas-harmonize-hub","version":"0.1.3","license":null,"protocols":["mcp"],"tags":["agents","allele-alignment","bioinformatics","gwas","harmonization","liftover","mcp","summary-statistics","sumstats"],"pricing":null,"endpoints":[{"url":"pypi:gwasharmonizer-mcp","type":"package_pypi","auth":null,"probeable":false}],"skills":null,"tools":null,"extra":null,"attribution":{"kind":"pypi","name":"pypi","repoUrl":"pypi","summary":"pypi","version":"pypi","description":"pypi","homepageUrl":"pypi"}},"derived":{"capabilities":[{"slug":"content.writing","name":"Writing & Editing","confidence":1,"provenance":"derived"}],"categories":["content"],"language":"en"},"observed":{"status":"unknown","statusReason":"Distributed as a package to run locally; no network endpoint to check.","lastOkAt":null,"lastProbedAt":null,"statusComputedAt":null,"reliability30d":null,"latestObservations":[],"tools":null,"package":{"name":"gwasharmonizer-mcp","registry":"pypi","observedAt":"2026-11-05T21:26:42.523Z","publishedAt":"2026-09-22T07:30:31.817035Z","latestVersion":"0.1.3"},"toolSurface":null,"endpointFacts":[]},"verification":{"claimed":false,"claimedAt":null,"proofs":[]},"provenance":{"sources":[{"source":"pypi","key":"gwasharmonizer-mcp","url":"https://pypi.org/project/gwasharmonizer-mcp/","firstSeenAt":"2026-09-24T10:27:35.028Z","fetchedAt":"2026-11-05T21:25:39.627Z","normalizedAt":"2026-11-05T21:25:39.627Z"}]},"firstSeenAt":"2026-09-24T10:27:35.028Z","updatedAt":"2026-11-05T21:26:42.523Z"}