SeqArray-a storage-efficient high-performance data format for WGS variant calls.
BACKGROUND
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.


METHODS
http://www.bioconductor.org/packages/SeqArray.


BACKGROUND
zhengx@u.washington.edu.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Biostatistics, University of Washington, Seattle, WA, USA.
Xiuwen
X
Zheng
Department of Biostatistics, University of Washington, Seattle, WA, USA.
Stephanie M
SM
Gogarten
Bioinformatics and Computational Biology, Genentech, Inc, South San Francisco, CA, USA.
Michael
M
Lawrence
Department of Biostatistics, University of Washington, Seattle, WA, USA.
Adrienne
A
Stilp
Department of Biostatistics, University of Washington, Seattle, WA, USA.
Matthew P
MP
Conomos
Department of Biostatistics, University of Washington, Seattle, WA, USA.
Bruce S
BS
Weir
Department of Biostatistics, University of Washington, Seattle, WA, USA.
Cathy
C
Laurie
Department of Biostatistics, University of Washington, Seattle, WA, USA.
David
D
Levine
D044962:Data Compression / Q000379:methods*; D014644:Genetic Variation; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D006801:Humans; D012984:Software; D000073336:Whole Genome Sequencing / Q000379:methods*