xAtlas

Overview

xAtlas is a fast and scalable small variant caller that has been developed at the Baylor College of Medicine Human Genome Sequencing Center.

Building

xAtlas requires the following software components to build:

• CMake (version 3.0 or higher required)
• HTSlib (version 1.6 or higher recommended)
• libpthread (included with most Unix-like systems)

xAtlas can be built using CMake by running the following commands from the base directory:

$ mkdir build
$ cd build
$ cmake ..
$ make

If HTSlib is installed in a location outside of CMake's library search path, the HTSlib install prefix can be set for the CMake command by defining the CMake variable HTSLIB_PREFIX:

$ cmake -DHTSLIB_PREFIX=/path/to/htslib-1.x ..

Usage

For example usage, see GettingStarted.