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Minimac

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'''You may want to learn about new and improved [[Minimac4]].'''
 
'''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.
= Download =
A binary Linux (64 bit) version of minimac is available [http://wwwcsg.sph.umich.edu/csg/cfuchsb/minimac-beta-2013.7.17.tgz from here] and source code [http://wwwcsg.sph.umich.edu/csg/cfuchsb/minimac.src.tgz from here]
The current version of minimac should be stamped 2013.7.17 - if your version shows a different version number or date stamp when it runs, it is not current.
=== Preparing Your Data ===
To get started, you will need to store your data in [[Merlin]] format pedigree and data files, one per chromosome. For details, of the Merlin file format, see the [http://wwwcsg.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html Merlin Tutorial].
Within each file, markers should be stored by chromosome position. Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele).
|-
|style=white-space:nowrap|<code>-d sample.dat</code>
| Data file in [http://wwwcsg.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html Merlin format]. Markers should be listed according to their order along the chromosome.
|-
| <code>-p sample.ped</code>
| Pedigree file in [http://wwwcsg.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html Merlin format]. Alleles should be labeled on the forward strand.
|-
| <code>--states 200</code>
|-
| <code>--refHaps ref.hap.gz </code>
| Reference haplotypes (e.g. from [http://wwwcsg.sph.umich.edu/csg/abecasis/MACH/download/ MaCH download page])
|-
| <code>--vcfReference </code>
=== Reference Haplotypes ===
Reference haplotypes generated by the 1000 Genomes project and formatted so that they are ready for analysis are available from the [http://wwwcsg.sph.umich.edu/csg/abecasis/MACH/download/ MaCH download page]. As of this writing, the most recent set of haplotypes are based on genotype calls were generated in May 2011 and are an interim analysis of Project's Phase I data.
=== Imputation quality evaluation ===
= Post-imputation Association Analysis =
== Quantitative Traits ==
Please use [http://wwwcsg.sph.umich.edu/csg/yli/mach/download/mach2qtl.source.V108.tgz mach2qtl].
== Binary Traits ==
Please use [http://wwwcsg.sph.umich.edu/csg/yli/mach/download/mach2dat.source.1.0.18.tgz mach2dat]. Versions 1.0.18 and above accommodate to minimac output.
= Reference =
If you use [[minimac]] or [[minimac2]] please cite:
Fuchsberger C, Abecasis GR, Hinds DA. minimac2: faster genotype imputation. Bioinformatics 2014 (accepted)[http://bioinformatics.oxfordjournals.org/content/early/2014/10/22/bioinformatics.btu704.short]
Howie B, Fuchsberger C, Stephens M, Marchini J, and Abecasis GR.
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