├── .gitignore ├── 00_archive └── example_info_files │ ├── bin_pheno.txt │ ├── info.txt │ ├── pop.txt │ ├── quantitative_pheno.txt │ └── regions.txt ├── 01_scripts ├── 01_config.sh ├── 02_list_bamfiles.sh ├── 03_saf_maf_gl_all.sh ├── 03_saf_maf_gl_prunedSNP.sh ├── 04_pca.sh ├── 04_pca_prunedSNP.sh ├── 05_ngs_admix.sh ├── 05_ngs_admix_pruned.sh ├── 06_saf_maf_by_pop.sh ├── 07_fst_by_group.sh ├── 08_thetas_by_pop.sh ├── 09_gwas_bin.sh ├── 09_gwas_quant.sh ├── 10A_cov_by_window.sh ├── 10B_pca_lostruct.sh ├── 10C_pca_mds_cluster.sh ├── 10D_pca_chosen_regions.sh ├── 11_plink_pruning_using_sites.sh ├── 12AbyLG_ngsLDprep.sh ├── 12Afusion_ngsLDprep.sh ├── 12BbyLG_ngsLDrun_simplify.sh ├── 12Bfusion_ngsLD.sh ├── 12Cfusion_simplifyLD.sh ├── 12DbyLG_ngsLD_bygroup.sh ├── 12Dfusion_ngsLD_bygroup.sh ├── 13_hwe.sh ├── Rscripts │ ├── Hobs_sliding.r │ ├── local_pca_maxdepth.R │ ├── local_pca_mds_all_chr_maxdepth_speedy_version.R │ ├── make_pca_simple.r │ ├── make_site_list_pruned.r │ ├── make_sites_list_maxdepth_simple.R │ ├── outliers_clusters_mds_allLG.R │ ├── subset_ind_coordinates.r │ ├── subset_random_Nind.r │ ├── subset_random_Nind_12ngsLD.r │ ├── sum_sites_2dsfs.r │ ├── sum_sites_sfs.r │ ├── visu_local_pca.r │ ├── visualise_admix.r │ ├── visualise_fst.r │ └── visualise_pca.r ├── depth.sh ├── split_beagle_by_group.sh └── utility_scripts │ ├── beagle_positions_extract_to_file.py │ ├── beagle_sliding_window.py │ ├── beagle_sliding_window_bis.py │ ├── index_genome.bash │ ├── index_genome.sh │ ├── ld_by_blocks.py │ ├── ld_by_blocks_optimized.py │ ├── ld_by_blocks_optimized_gzinput.py │ └── lower_half_matrix.sh ├── 02_info ├── .gitignore ├── bin_pheno.txt ├── pop.txt └── quantitative_pheno.txt ├── 03_saf_maf_gl_all └── .gitignore ├── 04_pca └── .gitignore ├── 05_ngs_admix └── .gitignore ├── 06_saf_maf_by_pop └── .gitignore ├── 07_fst_by_pop_pair └── .gitignore ├── 08_thetas └── .gitignore ├── 09_gwas └── .gitignore ├── 10_pca_by_window └── .gitignore ├── 11_plink └── 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