yupinglin0301 / dosageconvertor

DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to other formats such as MaCH or PLINK.

DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to ther formats such as MaCH or PLINK.

Please note that this tool CANNOT handle missing values in the input files and may NOT work for non-Minimac3/4 VCF files.

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

Users should follow the following steps to compile DosageConvertor

Prerequisites

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

Installation

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.

Usage

                         --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 >>>