# The BEDTools suite

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

## The full list of bedtools sub-commands.

- 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

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