Oct 24, 2014

minimac2: faster genotype imputation

Bioinformatics
Christian FuchsbergerDavid A Hinds

Abstract

Genotype imputation is a key step in the analysis of genome-wide association studies. Upcoming very large reference panels, such as those from The 1000 Genomes Project and the Haplotype Consortium, will improve imputation quality of rare and less common variants, but will also increase the computational burden. Here, we demonstrate how the application of software engineering techniques can help to keep imputation broadly accessible. Overall, these improvements speed up imputation by an order of magnitude compared with our previous implementation. minimac2, including source code, documentation, and examples is available at http://genome.sph.umich.edu/wiki/Minimac2

Mentioned in this Paper

Genome-Wide Association Study
Genome
Computer Programs and Programming
Programming Languages
Single Nucleotide Polymorphism
Genotype Determination
Computational Molecular Biology

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