ARCHIVED: About PLINK 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 ARCHIVED: Carbonate.

To add PLINK to your environment, load the plink module; for instructions, see Use modules to manage your software environment on IU research supercomputers.

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.

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

• Citing PLINK
• Sources of funding to acknowledge in published work if you use IU's research cyberinfrastructure

For full documentation, see the PLINK website.