Table 1.

Summary of supported operations available in the BEDTools suite

Utility	Description
intersectBed*	Returns overlaps between two BED files.
pairToBed	Returns overlaps between a BEDPE file and a BED file.
bamToBed	Converts BAM alignments to BED or BEDPE format.
pairToPair	Returns overlaps between two BEDPE files.
windowBed	Returns overlaps between two BED files within a user-defined window.
closestBed	Returns the closest feature to each entry in a BED file.
subtractBed*	Removes the portion of an interval that is overlapped by another feature.
mergeBed*	Merges overlapping features into a single feature.
coverageBed*	Summarizes the depth and breadth of coverage of features in one BED file relative to another.
genomeCoverageBed	Histogram or a ‘per base’ report of genome coverage.
fastaFromBed	Creates FASTA sequences from BED intervals.
maskFastaFromBed	Masks a FASTA file based upon BED coordinates.
shuffleBed	Permutes the locations of features within a genome.
slopBed	Adjusts features by a requested number of base pairs.
sortBed	Sorts BED files in useful ways.
linksBed	Creates HTML links from a BED file.
complementBed*	Returns intervals not spanned by features in a BED file.

Utilities in bold support sequence alignments in BAM. Utilities with an asterisk were compared with Galaxy and found to yield identical results.