VICES

VICES (Verify Intensity Contamination from Estimated Sources) is a program that jointly estimates contamination and its sources in genotyping arrays.

Users should follow the following steps to compile VICES

<<< SEE https://genome.sph.umich.edu/wiki/VICES FOR DOCUMENTATION >>>

Prerequisites

Automatic installation of VICES 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 VICES is to use cget as follows:

cget install --prefix <install_prefix> gjmzajac/VICES

Alternatively, you can setup a dev environment cmake directly.

cd vices
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 VICES command line for contamination estimation is as follows

./vices -r reports_list.txt \
        -o contam_estimates.txt

Here reports_list.txt is a text file with paths to Illumina report files containing array intensity information and contam_estimates.txt is the output.