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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 (for example, study design and planning, generating genotype calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.


  • Installed on the cluster.
    • To run plink on the cluster, you will need to use `module load plink` command to load the required binaries in your path.
    • This will load the most current plink version. If you want an older version, you can load that by using `module load plink/xx`, where xx is the version number.
    • To look at all the available modules, use `module avail` command.
    • gPlink can be run the easy way using X-server software on your local machine.


More information

Although BMI doesn't directly support this software, we encourage its use and will try to answer questions should they arise.  Simply send email to the BMI Help Desk