ARCHIVED: What is IMPUTE2, and how do I use it on Quarry at IU?

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Note: After seven years of production service, Indiana University's Quarry research computing cluster was decommissioned January 30, 2015. IU students, faculty, and staff can request accounts on Karst, IU's newest high-throughput computing cluster; for instructions, see ARCHIVED: Requesting an account. User data on Quarry has not be removed; you can access your old home directory data on Quarry from your account on any other IU research computing resource (see Available access to allocated and short-term storage capacity on IU's research systems). All software modules that were available on Quarry are available on Karst. If you have questions or concerns about Quarry's retirement, or need help, contact the High Performance Systems group.

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About IMPUTE2

IMPUTE version 2 (IMPUTE2) is a program for predicting unobserved genotypes based upon observed/known haplotypes in genome-wide case-control studies. For detailed information, see the IMPUTE2 home page.

Using IMPUTE2 on Quarry

At Indiana University, IMPUTE2 is available on Quarry. To use IMPUTE2 on Quarry, load the IMPUTE2 module:

  module load impute2

If your job will run for fewer than 20 minutes, call IMPUTE2 in the directory that contains the input files. If your job will take longer than 20 minutes, use the serialjob script to submit batch jobs; see ARCHIVED: At IU, how do I use the serialjob script to submit batch jobs on Quarry?

The output file will be generated in the same directory as the input files.

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Last modified on 2023-04-21 16:58:35.