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BEDOPS(1) User Commands BEDOPS(1)


bedops - manual page for bedops 2.4.35+dfsg


2.4.35 (typical)
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.

Error check input files (slower).
Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.
Print this message and exit successfully.
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.
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)


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.

October 2018 bedops 2.4.35+dfsg