What is PLINK, and where is it available at IU?

PLINK an open-source whole genome association analysis toolset for performing computationally efficient large-scale analyses of genotype/phenotype data. PLINK provides the following functions:

  • Data management
  • Summary statistics for quality control
  • Population stratification detection
  • Basic association testing
  • Multi-marker predictors
  • Haplotypic tests
  • Copy number variant analysis

PLINK does not support study design, genotype generation, or the visualization, annotation, or storage of results. Using a package such as R is recommended for visualizing and tabulating PLINK output.

At Indiana University, PLINK is available on Karst.

To add PLINK to your environment on Karst, load the plink module; for instructions, see On the research computing systems at IU, how do I use Modules to manage my software environment?

If your job will run for fewer than 20 minutes, run plink from the command line in the directory where your input files are located. If your job will take longer than 20 minutes, submit a batch job. The output file will be generated in the same directory as the input files.

Note:
When you launch PLINK for the first time, it will check online for an updated version. After checking, PLINK writes the .pversion file to the working directory and uses this cached information for the rest of the day. You can disable this behavior by launching PLINK with the --noweb option.

Any scholarly printed works, web pages, talks, online publications, and other presentations resulting from your use of PLINK on Karst should contain appropriate acknowledgment statements; see:

For full documentation, see the PLINK website.

Support for IU research computing systems, software, and services is provided by the Research Technologies division of UITS. To ask a question or get help, contact UITS Research Technologies.

This is document ayla in the Knowledge Base.
Last modified on 2017-06-20 17:18:42.

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