# Install bedtk with Homebrew

Simple toolset for BED files. Version 1.2 via Homebrew; verified from local package data.

## Install

```sh
sudo av install brew:bedtk
```

Additional install commands:

### macOS

- Homebrew (100%):

```sh
brew install bedtk
```

  Evidence: local Homebrew formula metadata

## Package facts

- **Package key:** brew:bedtk
- **Package manager:** Homebrew
- **Package manager page:** <https://formulae.brew.sh/formula/bedtk>
- **Version:** 1.2
- **Source summary:** Simple toolset for BED files
- **Homepage:** <https://github.com/lh3/bedtk>
- **Repository:** <https://github.com/lh3/bedtk>
- **License:** MIT
- **Source archive:** <https://github.com/lh3/bedtk/archive/refs/tags/v1.2.tar.gz>
- **Generated:** 2026-08-04T22:13:35+00:00

## Executables

- bedtk (cli)
- bedtk (alias)

## Install behavior

- Post-install hook: not defined
- Bottle: available on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux

## Freshness

- Page generated: 2026-08-04
- Package-manager version: 1.2
- Local data: ok
- Upstream repository: https://github.com/lh3/bedtk
- Upstream latest detected: v1.2 (current)
- info: No package-manager update timestamp was available.
## Project history and usage

bedtk is Heng Li's compact command-line toolkit for BED files, focused on fast interval overlap operations with a smaller scope than bedtools.

### Project history

The bedtk repository was created in October 2019, with the first visible commit adding interval intersection. Its README describes a simple BED toolset implementing intersection, subtraction, sorting, merging, and breadth-of-coverage calculations.

The project is tied to the 2021 Bioinformatics article 'Bedtk: finding interval overlap with implicit interval tree,' which explains its algorithmic focus. Upstream releases reached v1.0 in April 2025 and v1.2 in August 2025.

### Adoption history

The supplied package metadata lists Homebrew packaging. Upstream positions bedtk as a narrow, performance-oriented companion rather than a complete bedtools replacement.

### How it is used

bedtk is used for operations such as filtering overlapping or non-overlapping BED/VCF records, intersection without pre-sorting, coverage breadth, sorting, and merging.

### Why package nerds care

bedtk is notable because it comes from the lh3 bioinformatics tool lineage and deliberately keeps the surface area small. It is the kind of package a genomics CLI user installs when they care about speed and memory more than a broad command catalog.

### Timeline

- 2019: Repository created and initial intersection work committed.
- 2021: bedtk paper published in Bioinformatics.
- 2025: v1.0, v1.1, and v1.2 releases published.

### Related projects

- bedtools is explicitly named by upstream as broader and more versatile.
- cgranges is linked from the README and is related to the interval-overlap implementation family.

### Sources

- <https://api.github.com/repos/lh3/bedtk>
- <https://github.com/lh3/bedtk#readme>
- <https://github.com/lh3/bedtk/releases>
- source_facts.package-manager


## Security Notes

narrow executable package without higher-risk signals.

- **Geiger risk:** green / low
- narrow executable package without higher-risk signals

## Source Database Details

- **Source Database:** Homebrew formula API
- **Tap:** homebrew/core
- **Full Name:** bedtk
- **Version Scheme:** 0
- **Revision:** 0
- **Bottle Stable Root URL:** <https://ghcr.io/v2/homebrew/core>
- **Deprecated:** no
- **Disabled:** no
- **Keg Only:** no
- **URL Keys:** stable


## Related links

- [Source-control packages](https://pkg.so/source-control-tools/) - Belongs to a source-control command family.
- [Terminal utility packages](https://pkg.so/terminal-utilities/) - Matched terminal and command-line workflow metadata.
- [Networking and protocol packages](https://pkg.so/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata.
- [Scientific computing packages](https://pkg.so/scientific-computing-tools/) - Matched scientific computing metadata.
- [bedtools](https://pkg.so/brew/bedtools/) - Shares pkgdb curated category or tags: bed, bioinformatics, cli, genomics, science.
- [bedops](https://pkg.so/brew/bedops/) - Shares pkgdb curated category or tags: bed, bioinformatics, cli, genomics, science.
- [samtools](https://pkg.so/brew/samtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [blast](https://pkg.so/brew/blast/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [minimap2](https://pkg.so/brew/minimap2/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [bbtools](https://pkg.so/brew/bbtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [sambamba](https://pkg.so/brew/sambamba/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [abricate](https://pkg.so/brew/abricate/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.

## Combined YAML source

View the package source record on GitHub. [combined/bedtk.yml](https://github.com/mxcl/pkgdb/blob/main/combined/bedtk.yml)


## Sources

- pkg.so package database
- Geiger risk classifier
- package-page enrichment
- curated package history
- package version freshness
- pkgdb category and tag curation
- package relationship graph
- cross-ecosystem install command graph