Fast and accurate genotype imputation in genome-wide association studies through pre-phasing

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Next-generation genotype imputation service and methods (2016, methodology): “9) by carrying out genotype imputation into 100 individuals of European ancestry using reference panels of 1,091 to 32,390 sequenced individuals ( Table 1 and Online Methods).”
Robust inference with knockoffs (2018, methodology): “Returning to our genetic example, it has been shown that the joint distribution of SNPs may be accurately modeled by hidden Markov models (see [14, 16, 12, 10] for some early formulations), and there certainly is an abundance of genotype data to estimate the various model parameters; compare for ins”
Reference-based phasing using the Haplotype Reference Consortium panel (2016, background): “For such cohorts, we expect that cohort-based phasing may remain the preferred option due to ease of execution—although reference sizes are growing, and if the end goal is HRC-based imputation, then we expect that HRC-based pre-phasing [26] will be more convenient.”
Minimac2: Faster Genotype Imputation (2015, methodology): “Genotype imputation is routinely used to increase the power of genome-wide association studies (GWAS; Howie et al. , 2012; Li et al. , 2009; Marchini et al. , 2007).”
A one penny imputed genome from next generation reference panels (2018, background): “5k – 10M) and target sample sizes (10-1000) considered.”