bedtools

Analyze and manipulate genomic interval data

TLDR

Intersect genomic intervals

$ bedtools intersect -a [file1.bed] -b [file2.bed]

Merge overlapping intervals

$ bedtools merge -i [sorted.bed]

Sort BED file

$ bedtools sort -i [unsorted.bed]

Get coverage

$ bedtools coverage -a [regions.bed] -b [reads.bam]

Subtract intervals

$ bedtools subtract -a [all.bed] -b [exclude.bed]

Find closest features

$ bedtools closest -a [query.bed] -b [reference.bed]

Extract FASTA sequences for intervals

$ bedtools getfasta -fi [genome.fa] -bed [regions.bed]

bedtools is a suite of utilities for analyzing genomic intervals in BED, BAM, VCF, and GFF formats. It provides fast operations on genome annotations including intersection, merging, counting, and statistical analysis.The tool is essential for genomics research and comparative analysis of genomic features.

COMMANDS

intersect

Find overlapping intervals

merge

Combine overlapping intervals

coverage

Compute coverage statistics

subtract

Remove overlapping intervals

closest

Find nearest intervals

window

Find nearby intervals within window

sort

Sort BED/GFF/VCF files

genomecov

Compute genome-wide coverage

getfasta

Extract sequences from FASTA

bamtobed

Convert BAM to BED

slop

Extend intervals by a specified number of bases

flank

Create flanking intervals for each feature

complement

Return intervals not covered by features

COMMON PARAMETERS

-a file

First input file

-b file

Second input file

-wa

Write original A entry

-wb

Write original B entry

-f fraction

Minimum overlap fraction

-v

Report A entries without B overlap

-s

Require same strand

-S

Require opposite strand

-sorted

Use sorted algorithm for large files (lower memory)

-i file

Input file (used by merge, sort, etc.)

WORKFLOW

$ # Find genes overlapping SNPs
bedtools intersect -a genes.bed -b snps.bed

# Merge nearby features
bedtools merge -i features.bed -d 100

# Count reads in regions
bedtools coverage -a regions.bed -b reads.bam

# Extract promoter regions
bedtools flank -i genes.bed -g genome.txt -l 2000 -r 0

INSTALL

sudo apt install bedtools

yay -S bedtools

brew install bedtools

nix profile install nixpkgs#bedtools

CAVEATS

Some operations require sorted input. Large files consume significant memory. Coordinate systems (0-based vs 1-based) can cause off-by-one errors. Performance depends on file size and operation.

HISTORY

bedtools was created by Aaron Quinlan and Ira Hall, first released in 2010 as a comprehensive toolkit for genomic interval analysis.