Release of a much improved X chromosome analysis toolsest (XWAS v1.1)

We are excited to announce the release of a new XWAS version with a variety of new features, options, and several bug fixes. XWAS (chromosome X-wide Analysis toolSet) is a software suite for the analysis of the X chromosome in association analyses and similar studies. The new version, including a detailed manual, is available at The main improvements are outlined below:

XWAS version 1.1 inherits the features of version 1.0, with improved extensive quality control procedures that are tailored to the X chromosome. It removes related individuals in the sample in a fine-grained resolution to preserve as many individuals as possible. The new version also includes a convenient imputation procedure based on IMPUTE2. It also offers an array of additional statistical tests for X-linked markers, including: (1) a weighted regression test that accounts for the potential inflation in phenotypic variance due to X-inactivation in heterozygous females, (2) a test that combined that combines the above test with the previously implemented testfor inflated phenotypic variance, (3) Clayton's test for association on X chromosome in mixed-sex samples, (4) a modified epistasis test that uses a t-statistic for quantitative traits, (5) a convenient command "--run-all" to run several X-related tests at once, (6) for all single-marker tests, a version of gene-based test is now available that combines evidence from all variants in each X-linked gene, and (7) tests for gene-gene interaction on a gene-based level, which combine SNP-by-SNP interaction tests between all pairs of SNPs in two genes to produce a gene-level test for interaction between the two.

We also continually maintain our code and software. A couple of improvements that worth highlighting are:

1. We have added new and improved warning and error messages throughout so that it is easier to spot and correct any issues encountered while running XWAS.

2. We have fixed a bug in the sex difference test which can now output the p-value a single SNP.

The Keinan Lab will continue to update XWAS and new features/fixes will be distributed often. Future versions of the software will also consider sequence-based associations studies, with tests designed for testing rare variants on the X chromosome. Please join our mailing list by signing up on our website Please report bugs or ask questions by sending emails to We are also collaborating with several groups by running desired features of XWAS on their data, and we welcome additional such collaborations. Please email Alon Keinan ( regarding such collaborative opportunities.

Visit the XWAS project's web page where you will find the manual, download links, references, and related information. The software is freely available for download. 

A manuscript describing the earlier version of XWAS and its application can be found here, and a recent talk by Dr. Keinan on the subject here.