Provided by: bedops_2.4.35+dfsg-1_amd64
bedops - manual page for bedops 2.4.35+dfsg
bedops citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract https://doi.org/10.1093/bioinformatics/bts277 version: 2.4.35 (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)
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.