bedtools

Intersect genomic intervals

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

$ bedtools merge -i [sorted.bed]

$ bedtools sort -i [unsorted.bed]

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

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

bedtools command [options]

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.

intersect

Find overlapping intervals

Combine overlapping intervals

Compute coverage statistics

Remove overlapping intervals

Find nearest intervals

Find nearby intervals within window

Sort BED/GFF/VCF files

Compute genome-wide coverage

Extract sequences from FASTA

Convert BAM to BED

-a file

First input file

Second input file

Write original A entry

Write original B entry

Minimum overlap fraction

Report A entries without B overlap

Require same strand

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.

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

samtools(1), vcftools(1), bcftools(1)