Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis

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haptools

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Haptools is a collection of tools for simulating and analyzing genotypes and phenotypes while taking into account haplotype information. Haptools supports fast simulation of admixed genomes (with simgenotype), visualization of admixture tracks (with karyogram), simulating haplotype- and local ancestry-specific phenotype effects (with transform and simphenotype), and computing a variety of common file operations and statistics in a haplotype-aware manner.

Homepage: https://haptools.readthedocs.io/

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Arya R Massarat, Michael Lamkin, Ciara Reeve, Amy L Williams, Matteo D’Antonio, Melissa Gymrek, Haptools: a toolkit for admixture and haplotype analysis, Bioinformatics, 2023;, btad104, https://doi.org/10.1093/bioinformatics/btad104

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