Bedtools2.18

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.

While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

Module file

The module file can be found in this location:

 /cm/shared/modulefiles/SHARED/

<source lang='tcl'>

1. %Module1.0#######################################################################
   1. bedtools 2.18.0 modulefile

proc ModulesHelp { } {

       puts stderr "\tAdds bedtools v2.18.0 to your environment"

}

module-whatis "Adds bedtools v2.18.0 to your environment"

set bedtools_2180_root /cm/shared/apps/SHARED/bedtools/bedtools2.18.0/bin/

prepend-path PATH $bedtools_2180_root

</source>

Installation details

Compiled from source using gcc 4.4.

See also

• Globally installed software
• ABGC specific modules

External links

• Bedtools2 page on GitHub