run_projected_pca
This workflow is used to create a pca projection from a genetic reference dataset (in plink format, i.e., .bed/.bim/.fam). First, the reference data is subsetted to include only sites in common with a provided reference .bim (intended to contain only variants that one would expect to find in all downstream datsets that will be projected using loadings created in this worflow (e.g., a list of common sites that are easily imputed in TOPMed)), and then pruned for linkage equil
This is a companion discussion topic for the original entry at github.com/PRIMED-Ancestry-Inference/make_PCA_loadings/create_pca_projection