NAME

       bedops - manual page for bedops 2.4.41+dfsg

DESCRIPTION

       bedops

              citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract

              https://doi.org/10.1093/bioinformatics/bts277

       version:
              2.4.41 (typical)

       authors:
              Shane Neph & Scott Kuehn

              USAGE: bedops [process-flags] <operation> <File(s)>*

              Every  input file must be sorted per the sort-bed utility.  Each operation requires
              a minimum number of files as shown below.

              There is no fixed maximum number of files that may be used.

              Input files must have at least the first 3 columns of the BED  specification.   The
              program  accepts  BED  and Starch file formats.  May use '-' for a file to indicate
              reading from standard input (BED format only).

              Process Flags:

       --chrom <chromosome> Jump to and process data for given <chromosome> only.

       --ec   Error check input files (slower).

       --header
              Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.

       --help Print this message and exit successfully.

       --help-<operation>
              Detailed help on <operation>.  An example is --help-c or --help-complement

       --range L:R
              Add 'L' bp to all start coordinates and 'R' bp to end coordinates. Either value may
              be  +  or  -  to  grow  or  shrink  regions.   With the -e/-n operations, the first
              (reference) file is not padded, unlike all other files.

       --range S
              Pad or shrink input file(s) coordinates symmetrically by S.  This is shorthand for:
              --range -S:S.

       --version
              Print program information.

              Operations: (choose one of)

       -c, --complement [-L] File1 [File]*

       -d, --difference ReferenceFile File2 [File]*

       -e, --element-of [bp | percentage] ReferenceFile File2 [File]*

       by default, -e 100% is used.
              'bedops -e 1' is also popular.

       -i, --intersect File1 File2 [File]*

       -m, --merge File1 [File]*

       -n, --not-element-of [bp | percentage] ReferenceFile File2 [File]*

       by default, -n 100% is used.
              'bedops -n 1' is also popular.

       -p, --partition File1 [File]*

       -s, --symmdiff File1 File2 [File]*

       -u, --everything File1 [File]*

       -w, --chop [bp] [--stagger <nt>] [-x] File1 [File]*

              by default, -w 1 is used with no staggering.

       Example: bedops --range 10 -u file1.bed

              NOTE: Only operations -e|n|u preserve all columns (no flattening)

SEE ALSO

       The  full  documentation  for  bedops  is maintained as a Texinfo manual.  If the info and
       bedops programs are properly installed at your site, the command

              info bedops

       should give you access to the complete manual.