NAME¶

bedops - manual page for bedops 2.4.35+dfsg

DESCRIPTION¶

bedops

: citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
: https://doi.org/10.1093/bioinformatics/bts277

: 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.

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

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

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

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

-m, --merge File1 [File]*

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

-p, --partition File1 [File]*

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

-u, --everything File1 [File]*

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

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