macOS
Homebrewverified · 100%
brew install bedtklocal Homebrew formula metadata
brew / rank 13890
Install bedtk with Homebrew
Simple toolset for BED files. Version 1.2 via Homebrew; verified from local package data.
install
Additional install commands
overview
Package summary
Simple toolset for BED files
Project links
Commands and aliases
- bedtk
history
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 posture
Risk level: green
narrow executable package without higher-risk signals.
Risk classifier
green risk · low confidence · appliance
Why
- narrow executable package without higher-risk signals
Signals
- metadata:no-higher-risk-signals
Install behavior
- No Homebrew bottle metadata was recorded.
Recommended review
Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.
executables
Installed executables
| Command | Kind | Exposure | Note |
|---|---|---|---|
bedtk | executable | indexed executable | Discovered from the local executable index. |
freshness
Version and freshness
These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.
page generated2026-08-03
manager version1.2
manager updated
local dataunknown
upstreamnot available
latest detectednot detected
- okNo freshness warnings were generated.
install metadata
Package metadata
| Package key | brew:bedtk |
|---|---|
| Version | 1.2 |
| Package manager | Homebrew |
| Homepage | https://github.com/lh3/bedtk |
| Repository | https://github.com/lh3/bedtk |
| Bottle | not recorded |
| Service | none declared |
source trail
Generated from repository data
This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.
Combined YAML source
View the package source record on GitHub.
Used sources
- Geiger risk classifier
- cross-ecosystem install command graph
- curated package history
- pkg.so package database
- pkgdb category and tag curation