bedutils

General
	clean	Cleans a BED file (score should be integers)
	extend	Extends BED regions (3')
	nearest	Find the nearest annotation for a BED file (experimental)
	overlap	Find overlapping BED regions from a query and target file
	reduce	Merges overlapping BED regions
	refcount	Given a number of BED files, calculate the number of samples that overlap regions in a reference BED file
	sizes	Extract the sizes of BED regions
	sort	Sorts a BED file (in place)
	stats	Calculates simple stats for a BED file
	subtract	Subtracts one set of BED regions from another
Conversion
	annotate	Annotate BED files by adding / altering columns
	frombasecall	Converts a file in basecall format to BED3 format
	fromprimers	Converts a list of PCR primer pairs to BED regions
	fromvcf	Converts a file in VCF format to BED6
	tobed3	Removes extra columns from a BED (or BED compatible) file
	tobed6	Removes extra columns from a BED (or BED compatible) file
	tobedgraph	BED to BedGraph
	tofasta	Extract BED regions from a reference FASTA file
Misc
	cleanbg	Cleans up a bedgraph file