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