Difference between revisions of "Minimac"

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<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
 
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
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<!--Configuration-->
 
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{{#if: {{#var: conf}}|==Configuration==
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<!--Run-->
 
<!--Run-->
 
{{#if: {{#var: exe}}|==Additional Information==
 
{{#if: {{#var: exe}}|==Additional Information==
 
Minimac2 and Minimac3 are included in this module.
 
*Minimac module is listed under minimac/20130717
 
*Minimac2 module is listed under minimac/20140915
 
*Minimac3 module is listed under minimac/20150727
 
  
 
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[http://bioinformatics.oxfordjournals.org/content/early/2014/10/22/bioinformatics.btu704.short Fuchsberger C, Abecasis GR, Hinds DA. minimac2: faster genotype imputation. Bioinformatics 2014]
 
[http://bioinformatics.oxfordjournals.org/content/early/2014/10/22/bioinformatics.btu704.short Fuchsberger C, Abecasis GR, Hinds DA. minimac2: faster genotype imputation. Bioinformatics 2014]
  
[http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2354.html Howie B, Fuchsberger C, Stephens M, Marchini J, and Abecasis GR. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nature Genetics 2012]
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Howie B, Fuchsberger C, Stephens M, Marchini J, and Abecasis GR. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nature Genetics 2012.
  
 
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Latest revision as of 20:11, 18 August 2022

Description

minimac website  

Minimac is a low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. The name has two parts. The first, "mini", refers to the modest amount of computational resources it requires. The second, "mac", is short hand for MaCH, our widely used algorithm for genotype imputation.

Environment Modules

Run module spider minimac to find out what environment modules are available for this application.

System Variables

  • HPC_MINIMAC_DIR - installation directory




Citation

If you publish research that uses minimac you have to cite it as follows:

Fuchsberger C, Abecasis GR, Hinds DA. minimac2: faster genotype imputation. Bioinformatics 2014

Howie B, Fuchsberger C, Stephens M, Marchini J, and Abecasis GR. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nature Genetics 2012.