# 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:** - **Version:** 1.2 - **Source summary:** Simple toolset for BED files - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** MIT - **Source archive:** - **Generated:** 2026-07-10T07:20:53+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: 2026-07-10 - 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 - - - - 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:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** stable ## Related links - [Source-control packages](https://www.automicvault.com/pkg/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://www.automicvault.com/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://www.automicvault.com/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [vcfanno](https://www.automicvault.com/pkg/brew/vcfanno/) - Shares av.db curated category or tags: bed, bioinformatics, cli, science. - [abpoa](https://www.automicvault.com/pkg/brew/abpoa/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [abricate](https://www.automicvault.com/pkg/brew/abricate/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [abyss](https://www.automicvault.com/pkg/brew/abyss/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [adapterremoval](https://www.automicvault.com/pkg/brew/adapterremoval/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [alevin-fry](https://www.automicvault.com/pkg/brew/alevin-fry/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [any2fasta](https://www.automicvault.com/pkg/brew/any2fasta/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [augustus](https://www.automicvault.com/pkg/brew/augustus/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [fastq-tools](https://www.automicvault.com/pkg/brew/fastq-tools/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, files, science. - [sickle](https://www.automicvault.com/pkg/brew/sickle/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, files, science. - [vcflib](https://www.automicvault.com/pkg/brew/vcflib/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, files, science. ## Combined YAML source View the package source record on GitHub. [combined/bedtk.yml](https://github.com/automic-vault/db/blob/main/combined/bedtk.yml) ## Sources - Nucleus package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - av.db category and tag curation - package relationship graph - cross-ecosystem install command graph