Information about software packages installed on the ICHEC systems.
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). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.
PLINK (one syllable) is being developed by Shaun Purcell at the Center for Human Genetic Research (CHGR), Massachusetts General Hospital (MGH), and the Broad Institute of Harvard & MIT, with the support of others.
PLINK is available under the terms of the GNU Public License (GPL) version 2.
To use PLINK load the relevant environment module:
Further information can be obtained at PLINK Homepage.
How to cite PLINK:
If you use PLINK in any published work, please cite both the software (as an electronic resource/URL) and the manuscript describing the methods.
Package: PLINK (including version number)
Author: Shaun Purcell
PLINK: a toolset for whole-genome association and population-based linkage analysis.
American Journal of Human Genetics 81(3): 559-575.