Announcing XWAS version 3.0!


"Putting the X into sex chromosome research" (Cornell Chronicle, November 9, 2017)



The Keinan lab is pleased to announce the release of a new version of its XWAS software package (May 1, 2018), which offers brand new functionality and rich enhancements! XWAS (chromosome X-Wide Analysis toolSet) facilitates analysis of the X chromosome in genome-wide association studies and similar types of studies. The XWAS package offers standard GWAS procedures adapted specifically to X, including: sex-aware genotype calling from raw intensity data, extensive quality control for the X chromosome, sex-aware imputation, statistical association tests for X-linked markers and genes, gene-gene interaction testing for X and the autosomes, and a visualization suite for association results. XWAS 3.0 is open source, freely available for academic use, and is provided with a detailed manual and running examples. Visit the XWAS project’s web page to download.


What's new?

XWAS 3.0 is fully backwards compatible and supports all functionality from previous versions. New features in the version include:

  • X-wide genomic control for correcting unexpected inflation of test statistics.
  • A new visualization suite for the output of association tests, including auto-generated X-wide Manhattan plots, QQ-plots, and QQ-plots following genomic control correction.
  • A new tool for visualizing genotype array intensity information along with genotype calls, while highlighting differences between males and females; can help identify erroneous X-linked calls, such as false positives due to differential plate sex ratios.
  • An option to test all X variants concurrently with male genotype 0/1 coding (1 being equivalent to a female heterozygote) and 0/2 coding (i.e. a male genotype equivalent to either female homozygote).
  • Output of summary statistics of different association tests that include odds ratio or effect size with standard errors and confidence intervals.
  • Options to run fixed- and random-effects meta-analyses based on the above output from different XWAS runs.
  • Improved gene-gene interaction testing that considers all SNP-pairs between the genes of interest.
  • An option to run genotype calling in parallel, providing a crucial speed-up when very large samples are involved.
  • Finally, various bug fixes and user interface improvements.

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. 


Calling All XWAS Users!

For current XWAS users, we are putting together a paper describing the software and would like to cite your work and potentially discuss it. If of interest, please contact Alon Keinan ( for further details.