DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to ther formats such as MaCH or PLINK.
<<< SEE http://genome.sph.umich.edu/wiki/DosageConvertor FOR DOCUMENTATION >>>
Users should follow the following steps to compile DosageConvertor
Automatic installation of DosageConvertor 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
The easiest way to install DosageConvertor and its dependencies is to use the install.sh file provided.
cd DosageConvertor
bash install.sh
Alternatively, you can setup a dev environment cmake directly.
cd DosageConvertor
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.
--info TestDataImputedVCF.info
--prefix OutputFilePrefix
--type plink OR mach // depending on output format
--format DS or GP // based on if you want to output
// dosage (DS) or genotype prob (GP)
--buffer 10000 // Number of Markers to import and
// print at a time (valid only for
// MaCH format)
--idDelimiter _ // Delimiter to Split VCF Sample ID into
// FID and IID for PLINK format ```
<<< SEE http://genome.sph.umich.edu/wiki/DosageConvertor FOR DOCUMENTATION >>>