2.31.1

bedtools2 container

GitHub Repo: bedtools

Full documentation: https://bedtools.readthedocs.io/en/latest/index.html

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

List of sub-commands in bedtools 2.31.0:

• annotate
• bamtobed
• bamtofastq
• bed12tobed6
• bedpetobam
• bedtobam
• closest
• cluster
• complement
• coverage
• expand
• flank
• fisher
• genomecov
• getfasta
• groupby
• igv
• intersect
• jaccard
• links
• makewindows
• map
• maskfasta
• merge
• multicov
• multiinter
• nuc
• overlap
• pairtobed
• pairtopair
• random
• reldist
• shift
• shuffle
• slop
• sort
• subtract
• summary
• tag
• unionbedg
• window

Example Usage

# bedtools consists of a suite of sub-commands that are invoked as follows:
# bedtools [sub-command] [options]

# For example, to intersect two BED files, one would invoke the following:
bedtools intersect -a a.bed -b b.bed

More examples are found in the bedtools tutorial