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Nature Research, Nature Methods, 1(13), p. 63-65, 2015

DOI: 10.1038/nmeth.3654

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Efficient genotype compression and analysis of large genetic-variation data sets

Journal article published in 2015 by Ryan M. Layer, Neil Kindlon, Konrad J. Karczewski ORCID, Aaron R. Quinlan
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This paper is available in a repository.

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Abstract

Genotype 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.