Primarily Bash and R scripts to run various GWAS sample and snp-level QC, imputation preparation, PCA, and genome wide association testing steps using PLINK, SMARTPCA, RStats and Tidyverse visualization. Some additional scripts for performing colinearity and covariability analysis (using lares() in R) of clinical variables with genotype will also be added here once finalized
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Bash scripts provided here to run various GWAS QC, Imputation, PCA, and association testing steps using PLINK, SMARTPCA, RStats and Visualization
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