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

Abstract excerpt

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...

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