Genotype imputation Sample Clauses

Genotype imputation. In order to increase genotype information that can be used to customize the ref- erence genome, we turn to the genotyping imputation techniques that have been developed in the past five years and showed great success in finding association of untyped SNPs and disease phenotype in many GWAS studies [91, 92]. In this study, we used MaCH version 1.0 [84] and Minimac [89] programs to perform geno- type imputation. Default parameters are used for MaCH and Minimac throughout this pipeline. We use population-specific reference panels from the 1000 Genomes Project [69] which contains 25,802,094 SNPs for Yoruba in Ibadan, Nigeria (YRI) and 17,076,866 for Utah residents with ancestry from northern and western Europe (CEU). We use Rsq threshold of 0.7 for imputation quality control to balance the number of qualified genotypes and quality of imputation.
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Related to Genotype imputation

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