Plink
Description
PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data).
License
GNU GENERAL PUBLIC LICENSE v3
Usage
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 plink and load default version of plink as
module avail plink/ # list available modules module load plink # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail plink
and choose explicit version you want to use.
Documentation
Documentation is available on https://www.cog-genomics.org/plink/1.9/data or you can type plink --help