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Next Generation Sequencing analysis tools are no longer available through this interface. To run such analysis, please use Linux machines at BioHPC Lab.

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Version 1 Rev 494
(2015/05/29 16:42:52)

This interface is brand new. Please send comments to

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. is being developed by Shaun Purcell at the Center for Human Genetic Research (CHGR), Massachusetts General Hospital (MGH), with the support of others. For detailed information and references, visit the PLINK web page.

This interface allows you execute a set of independent PLINK tasks (just one or thousands of PLINK commands) in parallel. You will need to provide a list of PLINK tasks to execute and an archive file (in zip or tgz format) containing all input files referenced or implied by the PLINK command lines you submit. You may also select the compute cluster and the number of processors on which to run the job. If unsure about the cluster options, stick to the defaults.

Calculations will be carried out on the BioHPC compute cluster at CBSU. You will receive e-mail notifications when the job is submitted, when it starts, and when it is finished. Output will be available via links embedded in the notification e-mails. For more information about this program and BioHPC interface in general, please visit our Frequently Asked Questions page.

You will receive e-mail notifications once the job is submitted, when it starts, and when it is finished. During the run you will be able to monitor the standard output from the program using a link provided in a notification e-mail. Output files produced by individual PLINK tasks will be packed into separate zip archive files available through links in notification e-mails. Check out the important output file naming conventions. Upon the smooth ending of the job, a final single zip archive, containing all output files, will also be produced.  

(only guests need to use this field, registered users should log in) 

Job name:   

Provide a list of PLINK commands to execute
You can just type or paste them in (using the "paste" option), or you can upload a text file containing individual commands on separate lines (use the "upload" option). Example can be found here

upload text filepaste

Provide your input files (packed into a single zip or tgz archive file)
The archive must contain ALL input files referenced or implied by your PLINK commands (example). When the archive is unpacked, all files should end up in the current directory (i.e., the archive should not have any embedded directory structure). If the file is smaller than 10MBytes, you can upload it from your local machine using the "upload" option. An alternative (which works also for larger files) is to upload the file first to our FTP server and then use the "copy" option (please contact us for instructions on how to access the FTP server). Members of the COPD project can also use the COPD version of the "copy" option.

uploadcopy copy (COPD only)

Cluster: This application can't run at this time - no suitable clusters
or you are not authorized to use the service.
The service is available only to Cornell students, faculty, and staff.
( Show timeout info)

Max number of processors:

Application P-IPRSCAN under maintenance:
Application HapMap Reads under maintenance: