TY - JOUR T1 - Population Genotype Calling from Low-coverage Sequencing Data JF - bioRxiv DO - 10.1101/085936 SP - 085936 AU - Lin Huang AU - Petr Danecek AU - Sivan Bercovici AU - Serafim Batzoglou Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/08/11/085936.abstract N2 - In recent years, several large-scale whole-genome projects sequencing tens of thousands of individuals were completed, with larger studies are underway. These projects aim to provide high-quality genotypes for a large number of whole genomes in a cost-efficient manner, by sequencing each genome at low coverage and subsequently identifying alleles jointly in the entire cohort. Here we present Ref-Reveel, a novel method for large-scale population genotyping. We show that Ref-Reveel provides genotyping at a higher accuracy and higher efficiency in comparison to existing methods by applying our method to one of the largest whole-genome sequencing datasets presently available to the public. We further show that utilizing the resulting genotype panel as references, through the Ref-Reveel framework, greatly improves the ability to call genotypes accurately on newly sequenced genomes. In addition, we present a Ref-Reveel pipeline that is applicable for genotyping of very small datasets. In summary, Ref-Reveel is an accurate, scalable and applicable method for a wide range of genotyping scenarios, and will greatly improves the quality of calling genomic alterations in current and future large-scale sequencing projects. ER -