GWASTools: an R/Bioconductor package for quality control and analysis of genome-wide association studies

Bioinformatics. 2012 Dec 15;28(24):3329-31. doi: 10.1093/bioinformatics/bts610. Epub 2012 Oct 10.

Abstract

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 datasets 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 single nucleotide polymorphism annotation.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Genome-Wide Association Study / standards*
  • Genotype
  • Humans
  • Polymorphism, Single Nucleotide*
  • Quality Control
  • Software*