RT Journal Article
SR Electronic
T1 Sparse Project VCF: efficient encoding of population genotype matrices
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 611954
DO 10.1101/611954
A1 Michael F. Lin
A1 Xiaodong Bai
A1 William J. Salerno
A1 Jeffrey G. Reid
YR 2019
UL http://biorxiv.org/content/early/2019/04/17/611954.abstract
AB Summary Variant 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 Implementation Freely available at github.com/mlin/spVCFContact dna{at}mlin.net