What is PLINK, and how do I use it on Quarry at IU?

On this page:

• About PLINK
• Using PLINK on Quarry

About PLINK

PLINK is a tool set for genome association study focusing on analysis of genotype/phenotype data. It doesn't support study design, genotype generation, or the visualization, annotation, or storage of results.

PLINK provides the following functions: data management, summary statistics for quality control, population stratification detection, basic association testing, multimarker predictors, haplotypic tests, and copy number variant analysis. For information about these and other features, visit the PLINK home page.

Using PLINK on Quarry

At Indiana University, PLINK version 1.06 is available on Quarry. Accounts on Quarry are available to all IU students, faculty, and staff, as well as affiliated researchers. Instructional use is limited to courses approved by the Director for Research Technologies. Review the Quarry usage policies before requesting a Quarry account. For more, see Getting started on Quarry.

To use PLINK on Quarry, request a Quarry account if you don't have one, and then set up SoftEnv and submit jobs.

Request a Quarry account

To request a Quarry account, use the Account Management System (AMS); see At IU, if I already have some computing accounts, how do I get others?

Set up SoftEnv and submit jobs

1. To add PLINK to your SoftEnv, edit your ~/.soft file to add the line +plink-1.06 . Save the ~/.soft file and execute the resoft command.
   
   
2. If your job will run for fewer than 20 minutes, call PLINK in the directory where the input files are. If your job will take longer than 20 minutes, use the serialjob script to submit batch jobs.
   
   
3. The output file will be generated in the same directory where the input files are.

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