{
  "name": "genome.sh",
  "tagline": "The jq of genomics",
  "description": "Fast, open-source CLI and API for querying genetic variants across ClinVar, gnomAD, dbSNP, AlphaMissense, ClinGen, PharmGKB, and UniProt.",
  "license": "MIT",
  "lastUpdated": "2026-09-04",
  "install": {
    "cargo": "cargo install genome-sh",
    "conda": "conda install -c bioconda genome-sh",
    "binary": "genome"
  },
  "databases": [
    "ClinVar",
    "gnomAD",
    "dbSNP",
    "AlphaMissense",
    "ClinGen",
    "PharmGKB",
    "UniProt"
  ],
  "cli": {
    "repository": "https://github.com/romainsimon/genome-sh",
    "crate": "https://crates.io/crates/genome-sh",
    "commands": [
      {
        "name": "query",
        "usage": "genome query",
        "description": "Look up variants by rsID, coordinates, HGVS, or gene."
      },
      {
        "name": "annotate",
        "usage": "genome annotate",
        "description": "Annotate a VCF against the local database, streaming record by record."
      },
      {
        "name": "compare",
        "usage": "genome compare",
        "description": "Compare two genomes for shared, unique, and clinically significant variants."
      },
      {
        "name": "extract",
        "usage": "genome extract",
        "description": "Extract variants from CRAM or BAM files."
      },
      {
        "name": "predict",
        "usage": "genome predict",
        "description": "Opt-in AlphaGenome effect prediction. Requires an API key and explicit consent."
      },
      {
        "name": "db",
        "usage": "genome db",
        "description": "Install, update, and inspect the local variant database."
      },
      {
        "name": "config",
        "usage": "genome config",
        "description": "Set default format, reference genome, and optional AlphaGenome key."
      }
    ],
    "formats": [
      "human",
      "json",
      "compact"
    ]
  },
  "api": {
    "baseUrl": "https://api.genome.sh",
    "siteBaseUrl": "https://genome.sh/api/v1",
    "authentication": "none",
    "endpoints": [
      {
        "method": "GET",
        "path": "/v1/query/:query",
        "url": "https://api.genome.sh/v1/query/:query",
        "description": "Look up variants by rsID, gene name, genomic coordinates, or HGVS notation."
      },
      {
        "method": "GET",
        "path": "/v1/gene/:gene",
        "url": "https://api.genome.sh/v1/gene/:gene",
        "description": "List known variants for a gene symbol such as BRCA1."
      },
      {
        "method": "GET",
        "path": "/v1/gnomad/:rsid",
        "url": "https://api.genome.sh/v1/gnomad/:rsid",
        "description": "Fetch gnomAD population frequencies for an rsID."
      },
      {
        "method": "GET",
        "path": "/v1/sources",
        "url": "https://api.genome.sh/v1/sources",
        "description": "List bundled annotation sources and versions."
      },
      {
        "method": "GET",
        "path": "/v1/stats",
        "url": "https://api.genome.sh/v1/stats",
        "description": "Return database counts and pipeline freshness."
      },
      {
        "method": "GET",
        "path": "/v1/health",
        "url": "https://api.genome.sh/v1/health",
        "description": "Health check for the HTTP API."
      }
    ]
  },
  "privacy": {
    "rawGenomicFiles": "local-only",
    "publicIdentifiers": "cli-or-http",
    "alphagenome": "opt-in"
  },
  "agentJob": {
    "name": "private-dna-pdf-report",
    "prompt": "https://genome.sh/agent-prompt.txt",
    "template": "https://github.com/romainsimon/genome-sh/tree/main/docs/report-template",
    "output": "A4 PDF filled from a local DNA file using the genome CLI"
  },
  "links": {
    "website": "https://genome.sh/",
    "query": "https://genome.sh/query",
    "docs": "https://genome.sh/docs",
    "agentGuide": "https://genome.sh/docs/agent-guide.md",
    "agentPrompt": "https://genome.sh/agent-prompt.txt",
    "reportTemplate": "https://github.com/romainsimon/genome-sh/tree/main/docs/report-template",
    "llms": "https://genome.sh/llms.txt",
    "llmsFull": "https://genome.sh/llms-full.txt",
    "catalog": "https://genome.sh/genome-catalog.json",
    "cliRepository": "https://github.com/romainsimon/genome-sh",
    "websiteRepository": "https://github.com/romainsimon/genome.sh",
    "crates": "https://crates.io/crates/genome-sh"
  }
}