bedutils

General

 cleanCleans a BED file (score should be integers)
 extendExtends BED regions (3')
 nearestFind the nearest annotation for a BED file (experimental)
 overlapFind overlapping BED regions from a query and target file
 reduceMerges overlapping BED regions
 refcountGiven a number of BED files, calculate the number of samples that overlap regions in a reference BED file
 sizesExtract the sizes of BED regions
 sortSorts a BED file (in place)
 statsCalculates simple stats for a BED file
 subtractSubtracts one set of BED regions from another

Conversion

 annotateAnnotate BED files by adding / altering columns
 frombasecallConverts a file in basecall format to BED3 format
 fromprimersConverts a list of PCR primer pairs to BED regions
 fromvcfConverts a file in VCF format to BED6
 tobed3Removes extra columns from a BED (or BED compatible) file
 tobed6Removes extra columns from a BED (or BED compatible) file
 tobedgraphBED to BedGraph
 tofastaExtract BED regions from a reference FASTA file

Misc

 cleanbgCleans up a bedgraph file