Plink

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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

Homepage

https://www.cog-genomics.org/plink2