Population simulations for topological stratification of genotype data

These files contain 100 replicates each of three simulated scenarios: A three-population (CHB, YRI, CEU from the 1000 Genomes Project) out of Africa (OOA) model with neutral mutations. Each population has 1000 members. An admixture model with two source populations, one admixed population (with a 75%/25% ancestry from the source populations), and a fourth population. Each population has 1000 members. A 3x3 stepping-stone model with continuous migration between all populations. Each population has 500 members. The replicates are stored as VCFs. These files can be converted to numpy using scikit-allel and the command import allel allel.vcf_to_npz The code to generate these simulations can be found at: https://github.com/hmsnell/topstrat_popsims We have also included the top PCS and some sample UMAP files used for clustering with HDBSCAN. However feel free to experiment with different combinations of UMAP parameters.