GWASTool: A web pipeline for detecting SNP-phenotype associations.

The genome-wide association study (GWAS) aims to detect associations between individual single nucleotide polymorphisms (SNPs) or SNP interactions and phenotypes to decipher the genetic mechanism. Existing GWAS analysis tools have different focuses and advantages, but suffer a series of tedious and heterogeneous configurations for computation. It is inconvenient for researchers to simply choose and apply these tools, statistically and biologically analyze their results for different usages. To address these issues, we develop a user friendly web pipeline GWASTool for detecting associations, which includes simulation data generation, associated loci detection, result visualization, analysis and comparison. GWASTool provides a unified and plugin-able framework to encapsulate the heterogeneity of GWAS algorithms, simplifies the analysis steps and energizes GWAS tasks. GWASTool is implemented in Java and is freely available for public use at http://www.sdu-idea.cn/GWASTool. The website hosts a comprehensive collection of resources, including a user manual, description of integrated algorithms, data examples and standalone version for download.