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

ABSTRACT:

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

SUBMITTER: Zheng X 

PROVIDER: S-EPMC5860110 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature