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 http://keinanlab.cb.bscb.cornell.edu/content/xwas. 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 http://keinanlab.cb.bscb.cornell.edu/content/xwas. Please report bugs or ask questions by sending emails to keinanlab.xwas@gmail.com. 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 (alon.keinan@cornell.edu) 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.