1 Telenti, A. et al. Deep sequencing of 10,000 human genomes. Proc Natl Acad Sci U S A 113, 11901-11906, doi:10.1073/pnas.1613365113 (2016).
2 Van der Auwera, G. A. et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics 43, 11 10 11-33, doi:10.1002/0471250953.bi1110s43 (2013).
3 Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987-2993, doi:10.1093/bioinformatics/btr509 (2011).
4 Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38, e164, doi:10.1093/nar/gkq603 (2010).
5 Naslavsky, M. S. et al. Exomic variants of an elderly cohort of Brazilians in the ABraOM database. Hum Mutat 38, 751-763, doi:10.1002/humu.23220 (2017).
6 Manichaikul, A. et al. Robust relationship inference in genome-wide association studies. Bioinformatics 26, 2867-2873, doi:10.1093/bioinformatics/btq559 (2010).
7 Gogarten, S. M. et al. Genetic association testing using the GENESIS R/Bioconductor package. Bioinformatics 35, 5346-5348, doi:10.1093/bioinformatics/btz567 (2019).
8 Zhang, F. et al. Ancestry-agnostic estimation of DNA sample contamination from sequence reads. Genome Res 30, 185-194, doi:10.1101/gr.246934.118 (2020).
9 Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19, 1655-1664, doi:10.1101/gr.094052.109 (2009).
10 Gouveia, M. H. et al. Origins, Admixture Dynamics, and Homogenization of the African Gene Pool in the Americas. Mol Biol Evol 37, 1647-1656, doi:10.1093/molbev/msaa033 (2020).
11 Chang, C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4, 7, doi:10.1186/s13742-015-0047-8 (2015).
12 Zheng, X. et al. A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics 28, 3326-3328, doi:10.1093/bioinformatics/bts606 (2012).
13 Karczewski, K. J. et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434-443, doi:10.1038/s41586-020-2308-7 (2020).
14 Kalia, S. S. et al. Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics. Genetics in medicine : official journal of the American College of Medical Genetics 19, 249-255, doi:10.1038/gim.2016.190 (2017).
15 Gardner, E. J. et al. The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology. Genome Res 27, 1916-1929, doi:10.1101/gr.218032.116 (2017).
16 MacDonald, J. R., Ziman, R., Yuen, R. K., Feuk, L. & Scherer, S. W. The Database of Genomic Variants: a curated collection of structural variation in the human genome. Nucleic Acids Res 42, D986-992, doi:10.1093/nar/gkt958 (2014).
17 Castelli, E. C., Paz, M. A., Souza, A. S., Ramalho, J. & Mendes-Junior, C. T. Hla-mapper: An application to optimize the mapping of HLA sequences produced by massively parallel sequencing procedures. Hum Immunol 79, 678-684, doi:10.1016/j.humimm.2018.06.010 (2018).
18 Lima, T. H. A. et al. HLA-A promoter, coding, and 3'UTR sequences in a Brazilian cohort, and their evolutionary aspects. HLA 93, 65-79, doi:10.1111/tan.13474 (2019).
19 Souza, A. S. et al. HLA-C Genetic Diversity and Evolutionary Insights in Two Samples From Brazil and Benin. HLA, doi:10.1111/tan.13996 (2020).
20 Robinson, J. et al. IPD-IMGT/HLA Database. Nucleic Acids Res 48, D948-D955, doi:10.1093/nar/gkz950 (2020).
21 Zheng, X. et al. HIBAG--HLA genotype imputation with attribute bagging. Pharmacogenomics J 14, 192-200, doi:10.1038/tpj.2013.18 (2014).
22 Nunes, K. et al. HLA imputation in an admixed population: An assessment of the 1000 Genomes data as a training set. Hum Immunol 77, 307-312, doi:10.1016/j.humimm.2015.11.004 (2016).
23 Li, D., Liu, C.-M., Luo, R., Sadakane, K. & Lam, T.-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674-1676, doi:10.1093/bioinformatics/btv033 (2015).
24 Li, H. & Birol, I. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094-3100, doi:10.1093/bioinformatics/bty191 (2018).
25 Pruitt, K. D., Tatusova, T. & Maglott, D. R. NCBI reference sequences (RefSeq): a curated nonredundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35, D61-65, doi:10.1093/nar/gkl842 (2007).
26 Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357-359, doi:10.1038/nmeth.1923 (2012).
27 Marks, P. et al. Resolving the full spectrum of human genome variation using Linked-Reads. Genome Res 29, 635-645, doi:10.1101/gr.234443.118 (2019).
28 Bergström, A. et al. Insights into human genetic variation and population history from 929 diverse genomes. Science 367, eaay5012, doi:10.1126/science.aay5012 (2020).
29 Chaisson, M. J. P. et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nature communications 10, 1784, doi:10.1038/s41467-018-08148-z (2019).
30 Delaneau, O., Marchini, J. & Zagury, J. F. A linear complexity phasing method for thousands of genomes. Nat Methods 9, 179-181, doi:10.1038/nmeth.1785 (2011).
31 Delaneau, O., Howie, B., Cox, A. J., Zagury, J. F. & Marchini, J. Haplotype estimation using sequencing reads. Am J Hum Genet 93, 687-696, doi:10.1016/j.ajhg.2013.09.002 (2013).
32 Lowy-Gallego, E. et al. Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project [version 2; peer review: 2 approved]. Wellcome Open Research 4, doi:10.12688/wellcomeopenres.15126.2 (2019).
33 Howie, B. N., Donnelly, P. & Marchini, J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 5, e1000529, doi:10.1371/journal.pgen.1000529 (2009).
34 Kehdy, F. S. et al. Origin and dynamics of admixture in Brazilians and its effect on the pattern of deleterious mutations. Proc Natl Acad Sci U S A 112, 8696-8701, doi:10.1073/pnas.1504447112 (2015).
35 Zhao, H. et al. CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics 30, 1006-1007, doi:10.1093/bioinformatics/btt730 (2014).
36 Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81, 559-575, doi:10.1086/519795 (2007).
37 Conomos, M. P., Reiner, A. P., Weir, B. S. & Thornton, T. A. Model-free Estimation of Recent Genetic Relatedness. Am J Hum Genet 98, 127-148, doi:10.1016/j.ajhg.2015.11.022 (2016).
38 Turner, S. D. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. bioRxiv, 005165, doi:10.1101/005165 (2014).
39 Barrett, J. C., Fry, B., Maller, J. & Daly, M. J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263-265, doi:10.1093/bioinformatics/bth457 (2004).