ARCHIVED: What is MACH, 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.

MACH is a haplotyper that uses a Markov chain to infer long haplotypes or missing genotypes. You can use it to combine results of genome-wide association scans (GWSS) based on different genotyping platforms and increase the power of GWSS on a single platform. For more, see MACH home page on the University of Michigan's Center for Statistical Genetics website.

At Indiana University, MACH is available on Quarry. To see which version is currently available, at the command prompt on Quarry, enter:

  module avail mach

To add MACH to your environment on Quarry, load the MACH module:

  module load mach

If your job will run for fewer than 20 minutes, you can use MACH from the command line in the directory where the input files are located. 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.