Population-specific genotype imputations using minimac or IMPUTE2
- 30 July 2015
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Protocols
- Vol. 10 (9), 1285-1296
- https://doi.org/10.1038/nprot.2015.077
Abstract
This protocol describes how to perform SNP imputations for GWAS meta-analysis with the Genome of the Netherlands reference panel using Minimac or IMPUTE2. In order to meaningfully analyze common and rare genetic variants, results from genome-wide association studies (GWASs) of multiple cohorts need to be combined in a meta-analysis in order to obtain enough power. This requires all cohorts to have the same single-nucleotide polymorphisms (SNPs) in their GWASs. To this end, genotypes that have not been measured in a given cohort can be imputed on the basis of a set of reference haplotypes. This protocol provides guidelines for performing imputations with two widely used tools: minimac and IMPUTE2. These guidelines were developed and used by the Genome of the Netherlands (GoNL) consortium, which has created a population-specific reference panel for genetic imputations and used this reference to impute various Dutch biobanks. We also describe several factors that might influence the final imputation quality. This protocol, which has been used by the largest Dutch biobanks, should take approximately several days, depending on the sample size of the biobank and the computer resources available.This publication has 28 references indexed in Scilit:
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