Didn't yet analyze ChrX in your GWAS? We released XWAS version 2.0!



The Keinan lab is excited to announce the release of a new version of its XWAS software package, which offers new functionality, richer options and user experience, and....well, admittedly, bug fixes. XWAS (chromosome X-Wide Analysis toolSet) facilitates the analysis of the X chromosome in genome-wide association studies and similar types of studies. XWAS 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.

XWAS version 2.0 inherits all features of the previous version 1.1. Important new functionality includes the incorporation of a sex-aware genotype calling pipeline for the X chromosome from raw intensity data based on an Affymetrix genotype array. This pipeline, based on BIRDSUITE, detects and reports genotypes and their likelihoods for each SNP-by-individual combination. It formats this information into a dataset that the user can then use for detailed XWAS analysis, starting with extensive quality control tailored to the X chromosome. It further allows comparing and summarizing the differences from another set of genotype calls (potentially produced by a genotype caller that was not sex-aware), and visualization of the genotyping intensity clusters through Evoker, which can illustrate the importance of accounting for sex in calling genotypes in plates of mixed-sex. BIRDSUITE additionally calls common copy number polymorphisms and detects novel copy number variants.

Additionally, version 2.0 improves on the unique gene-based tests for gene-gene interactions. New functionality allows the user to input two sets of genes (or any other loci) and test for interaction between each gene in the first set and each gene in the second. One application can be for one set to include X-linked loci and the second set autosomal loci, both chosen based on any set of criteria. As before, it can also consider as input a single set and test for interaction between each pair of genes in the set. We also fixed a couple of bugs, one in the calculation of the correlation matrix and another in the permutation of simulations from which the significance level is derived.

XWAS version 2.0 features new options in the quality control pipeline that allow the user to run it in quiet, verbose, or debugging mode, thereby controlling what the software reports during and after each quality control step. The version also provides improved troubleshooting measures, including a new script that verifies the genome build of the input data and their strand alignment. It also includes improved examples, to which we added README files that guide the user more easily through the examples. Last but not least, the version introduces several bug fixes (thanks to those of you who reported some of them).

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. 

To download our previous release, visit the web page of our previous version XWAS v1.1.