When used in conjunction with R/Bioconductor packages, the SeqArray package provides users a flexible, feature-rich, high-performance programming environment for analysis of WGS variant data.<br><b>Availability and Implementation</b>: http://www.bioconductor.org/packages/SeqArray.<br><b>Contact</b>: zhengx@u.washington.edu.<br><b>Supplementary information</b>: Supplementary data are available at Bioinformatics online.<br>