THIS IS CURRENTLY BEING UPDATED. PLEASE DO NOT USE IT.
MetaMinimac
MetaMinimac is a tool to merge GWAS data imputed against different reference panels (using minimac4)
<<< SEE https://genome.sph.umich.edu/wiki/MetaMinimac FOR DOCUMENTATION >>>
Users should follow the following steps to compile MetaMinimac
Prerequisites
Automatic installation of MetaMinimac 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 MetaMinimac and its dependencies is to use the install.sh file provided.
cd MetaMinimac
bash install.sh
Alternatively, you can setup a dev environment cmake directly.
cd MetaMinimac
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 MetaMinimac command line for imputation is as follows
MetaMinimac -i ImputedPrefix1:ImputedPrefix2 \
-o testRunPrefix Here ImputedPrefix1 and ImputedPrefix1 are the prefixes of the same GWAS data imputed against different reference panels (using minimac4)