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

On this page:

• About IMPUTE
• Using IMPUTE on Quarry

About IMPUTE

IMPUTE is a program for predicting unobserved genotypes based upon observed/known haplotypes in genome-wide case-control studies. For detailed information, see the IMPUTE home page.

Using IMPUTE on Quarry

At Indiana University, IMPUTE version 1.0 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 IMPUTE 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 IMPUTE to your SoftEnv, edit your ~/.soft file, adding the line +impute-1.0 . Save the ~/.soft file and execute the resoft command.
   
   
2. If your job will run for fewer than 20 minutes, call IMPUTE 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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