Sparse Project VCF: efficient encoding of population genotype matrices

Abstract

SummaryVariant Call Format (VCF), the prevailing representation for germline genotypes in population sequencing, suffers rapid size growth as larger cohorts are sequenced and more rare variants are discovered. We present Sparse Project VCF (spVCF), an evolution of VCF with judicious entropy reduction and run-length encoding, delivering >10X size reduction for modern studies with practically minimal information loss. spVCF interoperates with VCF efficiently, including tabix-based random access. Availability and ImplementationFreely available at github.com/mlin/spVCF Contactdna@mlin.net