Diana Chang, Feng Gao, Alon Keinan
Summary: We present XWAS (chromosome X-Wide Analysis tool-Set)–a toolset specially designed for analysis of the X chromosome in association studies, both on the level of single markers and the level of entire genes. It further offers other X-specific analysis tools, including quality control (QC) procedures for X-linked data. We have applied and tested this software by carrying out several X-wide association studies of autoimmune diseases. Availability and Implementation: The XWAS software package, which includes scripts, the binary executable PLINK/XWAS and all source code is freely available for download from http://keinanlab.cb.bscb.cornell.edu/content/tools-data. PLINK/XWAS is implemented in C++ and other features in shell scripts and Perl. This software package is designed for Linux systems.