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README.md

Minimac4

Minimac4 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac/mininac2/minimac3.

<<< SEE http://genome.sph.umich.edu/wiki/Minimac4 FOR DOCUMENTATION >>>

Users should follow the following steps to compile Minimac4

Prerequisites

Automatic installation of Minimac4 requires cget and cmake v3.2. These prerequisites can be installed as follows:

Ubuntu 16.04

sudo apt-get install cmake python-pip python-dev
pip install cget

Ubuntu 14.04

sudo apt-get install software-properties-common
sudo add-apt-repository ppa:george-edison55/cmake-3.x
sudo apt-get update
sudo apt-get install cmake python-pip python-dev
pip install cget

MacOS

brew install cmake
sudo easy-install pip
pip install --user cget --ignore-installed six

Installation

The easiest way to install Minimac4 and its dependencies is to use the install.sh file provided.

cd Minimac4
bash install.sh

Alternatively, you can use cget as follows:

cget install --prefix <install_prefix> statgen/Minimac4

Alternatively, you can setup a dev environment cmake directly.

cd Minimac4
cget install -f ./requirements.txt                      # Install dependencies locally.
mkdir build && cd build                                 # Create out of source build directory.
cmake -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake .. # Configure project with dependency paths.
make                                                    # Build.

Usage

A typical Minimac4 command line for imputation is as follows

minimac4 --refHaps refPanel.m3vcf \
         --haps targetStudy.vcf \
         --prefix testRun

Here refPanel.m3vcf is the reference panel used in M3VCF format (e.g. 1000 Genomes), targetStudy.vcf is the phased GWAS data in VCF format, and testRun is the prefix for the output files.