bedtools — Genomic Interval Analysis Toolkit

Overview

bedtools is the standard toolkit for operating on genomic intervals in BED, BAM, GFF, and VCF formats. It solves the core problem of genome arithmetic: finding overlaps between feature sets, computing coverage, extracting sequences, merging adjacent regions, and annotating features with nearest neighbors. bedtools operates on sorted coordinate lists and runs at C speed, making it practical for whole-genome analyses.

When to Use

• Intersecting ChIP-seq peaks with gene annotations to find promoter-overlapping peaks
• Merging overlapping ATAC-seq peaks or called regions across replicates
• Computing read coverage depth over target capture regions
• Extracting FASTA sequences for motif discovery or primer design
• Finding the nearest gene to each regulatory element or variant
• Subtracting blacklist or repeat regions from peak calls
• Expanding genomic intervals by fixed distance (promoter regions)
• Use tabix instead for fast indexed queries of a single genomic region
• For normalized coverage bigWig tracks, use deeptools bamCoverage instead
• Use mosdepth instead for whole-genome per-base depth (10× faster)