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.
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There is no fixed maximum number of files that may be used.
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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
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Print this message and exit successfully.
- --help-<operation>
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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
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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.