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

On this page:

• About MACH
• Using MACH on Quarry

About MACH

MACH is a Markov-chain-based haplotyper. It can infer long haplotypes or missing genotypes. You can use it to combine results of genome-wide association scans (GWSS) based on different genotyping platform and to increase the power of GWSS on a single platform.

For help, see the Center for Statistical Genetics' MACH Input Files and Genotype Imputation.

Using MACH on Quarry

At Indiana University, MACH 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 MACH 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 MACH to your SoftEnv, edit your ~/.soft file to add the line +mach-1.0.16 . Save the ~/.soft file and execute the resoft command.
   
   
2. If your job will run for fewer than 20 minutes, call MACH 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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