I am a fresh man of bioinformatic. I have resequenced 100 individuals of one species, and plan to explore its genetic sturcture and funtional genes by GWAS. However, should i mask the repeat region in the whole genome reference before SNP calling? And if i want to run and calculate PCA, admixture, Pi, Tajimas'D, and FST value, should i use the whole genome reference or the masked whole genome reference? Thanks for everyone's help.