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.
.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 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.
Research computing support at IU is provided by the Research Technologies division of UITS. To ask a question or get help regarding Research Technologies services, including IU's research supercomputers and research storage systems, and the scientific, statistical, and mathematical applications available on those systems, contact UITS Research Technologies. For service-specific support contact information, see Research computing support at IU.
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Last modified on 2023-12-17 07:02:11.