MOTIVATION: Whole-genome sequencing (WGS) data are being generated at an 
unprecedented rate. Analysis of WGS data requires a flexible data format to 
store the different types of DNA variation. Variant call format (VCF) is a 
general text-based format developed to store variant genotypes and their 
annotations. However, VCF files are large and data retrieval is relatively slow. 
Here we introduce a new WGS variant data format implemented in the 
R/Bioconductor package 'SeqArray' for storing variant calls in an array-oriented 
manner which provides the same capabilities as VCF, but with multiple high 
compression options and data access using high-performance parallel computing.
RESULTS: Benchmarks using 1000 Genomes Phase 3 data show file sizes are 14.0 Gb 
(VCF), 12.3 Gb (BCF, binary VCF), 3.5 Gb (BGT) and 2.6 Gb (SeqArray) 
respectively. Reading genotypes in the SeqArray package are two to three times 
faster compared with the htslib C library using BCF files. For the allele 
frequency calculation, the implementation in the SeqArray package is over 5 
times faster than PLINK v1.9 with VCF and BCF files, and over 16 times faster 
than vcftools. 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.
AVAILABILITY AND IMPLEMENTATION: http://www.bioconductor.org/packages/SeqArray.
CONTACT: zhengx@u.washington.edu.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics 
online.