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

xAtlas requires a recent version of HTSlib (versions 1.3 and higher are known to work, version 1.4 or higher is suggested).

To build xAtlas, run:

autoconf
./configure
make

xAtlas multithreading support is enabled by running configure as:

./configure --enable-multithreading

xAtlas supports two types of multithreading. The -P option splits the processes for reading the input alignment, processing SNPs, and processing indels into three separate threads. The -t option allows a variable number of HTSlib decompression threads to be spawned.