Quality Control of Genotypes

Simple quality control is available for genotypes. In get_genotypes function, when quality_control=true, minor allele frequency MAF threshold, defaulting to 0.01, is used, and fixed loci are removed. In addition, missing genotypes will be replaced by column means if they are denoted as 9 . Users can also impute missing genotypes before the analysis.

using JWAS,JWAS.Datasets
genofile   = dataset("genotypes.csv")
genotypes  = get_genotypes(genofile, separator=',', quality_control=true, MAF=0.05);