title: Efficient genotype compression and analysis of large genetic-variation data sets.
abstract: Genotype Query Tools (GQT) is an indexing strategy that expedites analyses of genome-variation data sets in Variant Call Format based on sample genotypes, phenotypes and relationships. GQT's compressed genotype index minimizes decompression for analysis, and its performance relative to that of existing methods improves with cohort size. We show substantial (up to 443-fold) gains in performance over existing methods and demonstrate GQT's utility for exploring massive data sets involving thousands to millions of genomes. GQT can be accessed at https://github.com/ryanlayer/gqt.
authors.affiliation: Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA.
authors.forename: Ryan M
authors.initials: RM
authors.lastname: Layer
authors.affiliation: Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA.
authors.forename: Neil
authors.initials: N
authors.lastname: Kindlon
authors.affiliation: Analytical and Translational Genetics Unit, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Konrad J
authors.initials: KJ
authors.lastname: Karczewski
authors.affiliation: Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA.|Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah, USA.|USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, USA.
authors.forename: Aaron R
authors.initials: AR
authors.lastname: Quinlan
mesh_terms: D066264:Datasets as Topic; D014644:Genetic Variation; D005838:Genotype