Bedtools
Description
Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.
License
Use
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of bedtools and load default version of bedtools as
module avail bedtools/ # list available modules module load bedtools # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail bedtools
and choose explicit version you want to use.
This makes available the path to the program binaries and loads also the SAMtools module. NOTE: SAMtools will not be loaded
if you use module bedtools-2.25.0.
Documentation
http://bedtools.readthedocs.org/en/latest/index.html