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A typical Minimac3 command line would have the following parameter options:
= Introduction =
[http://genome.sph.umich.edu/wiki/Minimac3 '''Minimac3 '''] is a lower memory and more computationally efficient implementation of [http://genome.sph.umich.edu/wiki/Minimac2 minimac2]. It is an algorithm for genotypic imputation that works on phased genotypes (say from [http://genome.sph.umich.edu/wiki/MaCH MaCH]) and is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.
This wiki page is designed to give users a detailed explanation on Minimac3 Usage.
= Download =
'''Minimac3 ''' is available as an undocumented release version. The source files are available for download here and commonly used reference panels in <code>M3VCF</code> format are available for download in [[#Reference Panels for Download | Reference Panels]].
* To Download Minimac3
{| class="wikitable" border="1" cellpadding="2"
|- bgcolor="lightgray"
! Description
! Download Link
|-
| Minimac3 Executable
| [[Media : Minimac3.v1.0.0.binary.tar.gz | UNIX Users ]]
|-
| Minimac3-omp Executable (for parallel computing)
| [[Media : Minimac3.v1.0.0.binary-OMP.tar.gz | UNIX Users ]]
|-
| Minimac3 Source Files
| [[Media : Minimac3.v1.0.0.tar.gz | UNIX Users ]]
|}A typical Minimac3 command line would have the following parameter options:
Command Line Options:
Command Line Options:
PhoneHome : --noPhoneHome, --phoneHomeThinning [50]
PhoneHome : --noPhoneHome, --phoneHomeThinning [50]
= Usage =
The most typically used parameter options are explained below with [[#Examples|examples]]. See subsection below for detailed [[#List of Options |list of available options]].
The most typically used parameter options are explained below with [[#Examples|examples]]. See subsection below for detailed [[#List of Options |list of available options]].
