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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.

Environment Modules

Run module spider plink to find out what environment modules are available for this application.

System Variables

  • HPC_PLINK_DIR - installation directory
  • HPC_PLINK_BIN - executable directory

Additional Information

The API between 1.x and 2.x changed the command lines substantially

Version 1.x documentation:

Version 2.x documentation: