genome.sh
The jq of genomics. A local Rust CLI and open REST API for ClinVar, gnomAD, dbSNP, AlphaMissense, ClinGen, PharmGKB, and UniProt.
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genome query rs1799945
rs1799945 HFE chr6:26090951 Significance: Pathogenic Condition: Hereditary hemochromatosis Alleles: C > G Review: criteria provided, multiple submitters
ClinVar, gnomAD, dbSNP, AlphaMissense, ClinGen, PharmGKB, UniProt. All in one place.
Written in Rust. Local SQLite database. Queries return in milliseconds.
Query variants over HTTP. Build apps, scripts, and integrations on top of genome.sh.
Pipe, filter, and script. JSON, TSV, and human-readable output formats.
MIT licensed. Inspect the code, contribute, or fork it. Available on crates.io.
Your genetic data stays on your machine. No uploads, no tracking, no accounts.
Install once, then query anything.
Install locally
cargo install genome-sh, then genome db install lite. The annotation database lives on disk.
Query by identifier
Look up an rsID, a gene symbol, or genomic coordinates. JSON, compact, or human output.
Pipe into tools
Annotate a VCF, filter ClinVar significance, or call the HTTP API from a script. No API key.
Seven annotation sources, one local index.
The CLI builds these into SQLite on your machine. The HTTP API queries the same public identifiers.
What genome.sh is
genome.sh is an open-source command-line tool and REST API for querying genetic variants. It is built for developers, bioinformaticians, and anyone who wants ClinVar or gnomAD data in a terminal, a notebook, or an application.
The local CLI indexes ClinVar, gnomAD, dbSNP, AlphaMissense, ClinGen, PharmGKB, and UniProt in SQLite. Queries return in milliseconds. Raw VCF, BAM, CRAM, and consumer DNA files stay on your machine.
The HTTP API accepts only public identifiers: rsIDs, gene names, HGVS strings, and coordinates. It does not accept genome uploads. genome.sh reports public annotations. It is not a medical device.
CLI and API
Command line
Install from crates.io or Bioconda. The crate is genome-sh. The binary is genome. Use lite, standard, or full database tiers depending on whether you need ClinVar only or population frequencies.
cargo install genome-sh genome db install lite genome query rs1799945 genome query BRCA1 --format json
REST API
No authentication. Query variants over HTTPS and consume JSON. The same lookup is available on the website query page.
curl https://api.genome.sh/v1/query/rs1799945 curl https://api.genome.sh/v1/query/BRCA1?limit=5 curl https://api.genome.sh/v1/stats
Continue from what you need.
- Query variants↗rsID, gene, or coordinates in the browser
- API documentation↗REST endpoints, no API key
- Guides↗DNA, inheritance, SNPs, and local variant lookup
- Genetics library↗Educational pages for common variants
- Local VCF analysis↗Parse a file in the browser, nothing uploaded
- Annotation sources↗ClinVar, gnomAD, dbSNP, and the rest
- DNA report prompt↗Ask an agent to produce a private PDF from a local file
Get a DNA report
Copies a prompt that asks an agent to analyse a VCF or consumer DNA export with the genome CLI on this machine and fill the printable A4 report. Nothing is uploaded.
Questions
What is genome.sh?
A command-line tool and HTTP API for querying genetic variants. It is built for developers, bioinformaticians, and anyone who wants ClinVar or gnomAD data in a terminal or a script.
How do I look up a variant?
Install with cargo install genome-sh, then run genome query with an rsID, gene symbol, or genomic coordinates. You can also search from the website query page.
Does my DNA leave my computer?
Not if you use the CLI or the browser importer. Those keep VCF and related files on disk. The HTTP API only accepts public identifiers such as rsIDs, gene names, and coordinates.
Is there an API key?
No. The REST API is open. AlphaGenome prediction is a separate, opt-in CLI command that does require a key.
Is this medical advice?
No. genome.sh reports annotations from public databases. It is informational software, not a medical device or a substitute for clinical care.
Look up a variant.
Start in the browser, or install the CLI and keep genomes on disk.