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
- shuffle
- slop
- sort
- subtract
- tag
- unionbedg
- window
