GWASTools: an R/Bioconductor package for quality control and analysis of Genome-Wide Association Studies.

Publication Type:

Journal Article

Source:

Bioinformatics (Oxford, England) (2012)

Keywords:

October 2012, Public Health Sciences Division

Abstract:

SUMMARY: GWASTools is an R/Bioconductor package for quality control and analysis of Genome-Wide Association Studies (GWAS). GWASTools brings the interactive capability and extensive statistical libraries of R to GWAS. Data are stored in NetCDF format to accommodate extremely large data sets that cannot fit within R's memory limits. The documentation includes instructions for converting data from multiple formats, including variants called from sequencing. GWASTools provides a convenient interface for linking genotypes and intensity data with sample and SNP annotation.Availability and Implementation: GWASTools is implemented in R and is available from Bioconductor (http://www.bioconductor.org). An extensive vignette detailing a recommended work flow is included. CONTACT: sdmorris@uw.edu.