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Bioinformatics. 2015 Mar 1;31(5):782-4. doi: 10.1093/bioinformatics/btu704. Epub 2014 Oct 22.

minimac2: faster genotype imputation.

Author information

1
Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA and 23andMe, Inc., Mountain View, CA, USA.

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.

AVAILABILITY AND IMPLEMENTATION:

minimac2, including source code, documentation, and examples is available at http://genome.sph.umich.edu/wiki/Minimac2

PMID:
25338720
PMCID:
PMC4341061
DOI:
10.1093/bioinformatics/btu704
[Indexed for MEDLINE]
Free PMC Article

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