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.