@article {Chang009795, author = {Diana Chang and Feng Gao and Alon Keinan}, title = {XWAS: a toolset for genetic data analysis and association studies of the X chromosome}, elocation-id = {009795}, year = {2014}, doi = {10.1101/009795}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Summary We present XWAS (chromosome X-Wide Analysis tool-Set) {\textendash} 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.Contact: ak735{at}cornell.edu}, URL = {https://www.biorxiv.org/content/early/2014/09/29/009795}, eprint = {https://www.biorxiv.org/content/early/2014/09/29/009795.full.pdf}, journal = {bioRxiv} }