├── README.md ├── misc ├── batches.tsv ├── long_range_LD_intervals.txt └── uniq_batch_pairs.tsv ├── plots ├── eur_pbk_hetcheck_fstat_thresh02.pdf ├── eur_pbk_hetcheck_hetrate_dev_from_mean.pdf ├── eur_pbk_ibd_Z0.vs.Z1.pdf ├── eur_pbk_sexcheck_fstat_F02_M08.pdf ├── eur_pbk_sexcheck_fstat_F02_M08_ped.vs.snpsex.pdf ├── eur_pbk_unrel.PC1_PC2.pdf ├── eur_pbk_unrel.PC2_PC3.pdf ├── eur_pbk_unrel.PC3_PC4.pdf ├── eur_pbk_unrel.PC4_PC5.pdf ├── eur_pbk_unrel.PC5_PC6.pdf ├── eur_pbk_unrel_ref.PC1_PC2_by_pop.pdf ├── eur_pbk_unrel_ref.PC2_PC3_by_pop.pdf ├── eur_pbk_unrel_ref.PC3_PC4_by_pop.pdf ├── eur_pbk_unrel_ref.PC4_PC5_by_pop.pdf ├── eur_pbk_unrel_ref.PC5_PC6_by_pop.pdf ├── pbk_ref.PC1_PC2_by_predPop.pdf ├── pbk_ref.PC1_PC2_by_predPop0.9.pdf ├── pbk_ref.PC1_PC2_by_superpop.pdf ├── pbk_ref.PC2_PC3_by_predPop.pdf ├── pbk_ref.PC2_PC3_by_predPop0.9.pdf ├── pbk_ref.PC2_PC3_by_superpop.pdf ├── pbk_ref.PC3_PC4_by_predPop.pdf ├── pbk_ref.PC3_PC4_by_predPop0.9.pdf ├── pbk_ref.PC3_PC4_by_superpop.pdf ├── pbk_ref.PC4_PC5_by_predPop.pdf ├── pbk_ref.PC4_PC5_by_predPop0.9.pdf ├── pbk_ref.PC4_PC5_by_superpop.pdf ├── pbk_ref.PC5_PC6_by_predPop.pdf ├── pbk_ref.PC5_PC6_by_predPop0.9.pdf ├── pbk_ref.PC5_PC6_by_superpop.pdf └── snp_missRateDiff_btw_batch.pdf └── scripts ├── 01_callrate_qc_by_batch.sh ├── 02_plot_snp_missdiff_btw_batch.R ├── 02_plot_snp_missdiff_btw_batch.sh ├── 03_find_snp_missdiff_btw_batch.R ├── 03_find_snp_missdiff_btw_batch.sh ├── 04_makebed_initqc_by_batch.sh ├── 05_merge_batches.sh ├── 06_remove_dup_mono_snps.sh ├── 07_pca.sh ├── 08_classify_ancestry.R ├── 08_classify_ancestry.sh ├── 09_write_pop_plink.sh ├── 10_pop_check_sex.R ├── 10_pop_check_sex.sh ├── 11_pop_check_het.R ├── 11_pop_check_het.sh ├── 12_pop_filter_ibd.R ├── 12_pop_filter_ibd.sh ├── 13_pop_find_batch_assoc_snps.sh ├── 13_pop_run_batch_assoc.sh ├── 14_pop_pca.R ├── 14_pop_pca.sh ├── 15_pop_write_qc_plink.sh ├── 16_pop_prep_mis_imp.sh ├── 17_pop_write_qc_vcf.sh ├── 18_pop_annot_imp_vcf.sh ├── 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