bedtools ☆
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Description:
Tools for genome arithmetic (set theory on the genome)
Type: Formula  |  Latest Version: 2.31.1@0  |  Tracked Since: Dec 17, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: genomics bioinformatics command-line data-analysis science
Install: brew install bedtools
About:
bedtools is a powerful command-line utility suite for genome arithmetic, enabling set operations like intersection, union, and subtraction on genome annotation files (BED, GFF, VCF). It efficiently manipulates and analyzes large-scale genomic datasets, serving as a fundamental tool for bioinformaticians.
Key Features:
  • Efficiently intersects, merges, and counts genomic features
  • Supports multiple file formats (BED, GFF, VCF, SAM)
  • Fast set arithmetic on large genome files
  • Converts between different genomic file formats
Use Cases:
  • Identifying regulatory variants within coding regions
  • Counting sequencing reads overlapping gene annotations
  • Merging adjacent ChIP-seq peaks into consensus regions
Alternatives:
  • htslib – Library focused on reading/writing SAM/BAM/VCF, whereas bedtools focuses on arithmetic operations.
License: MIT
Dependencies: xz
Bottles available for: arm64_tahoe, arm64_sequoia, arm64_sonoma, arm64_ventura, arm64_monterey, sonoma, ventura, monterey, arm64_linux, x86_64_linux
Version History
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