Layer, Ryan M.Kindlon, NeilKarczewski, KonradQuinlan, Aaron R.2016-06-142015Layer, Ryan M., Neil Kindlon, Konrad J. Karczewski, and Aaron R. Quinlan. 2015. “Efficient genotype compression and analysis of large genetic variation datasets.” Nature methods 13 (1): 63-65. doi:10.1038/nmeth.3654. http://dx.doi.org/10.1038/nmeth.3654.1548-7091http://nrs.harvard.edu/urn-3:HUL.InstRepos:27320241Genotype Query Tools (GQT) is a new indexing strategy that expedites analyses of genome variation datasets in VCF format based on sample genotypes, phenotypes and relationships. GQT’s compressed genotype index minimizes decompression for analysis, and performance relative to existing methods improves with cohort size. We show substantial (up to 443 fold) performance gains over existing methods and demonstrate GQT’s utility for exploring massive datasets involving thousands to millions of genomes.en-USJournal Article2016-06-1410.1038/nmeth.3654