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. 2023 Mar 1;39(3):btad104.
doi: 10.1093/bioinformatics/btad104.

Haptools: a toolkit for admixture and haplotype analysis

Arya R Massarat  1 , Michael Lamkin  2 , Ciara Reeve  3 , Amy L Williams  4 , Matteo D'Antonio  5 , Melissa Gymrek  2   5   6
Affiliations

Haptools: a toolkit for admixture and haplotype analysis

Arya R Massarat et al. Bioinformatics. .

Abstract

Summary: Leveraging local ancestry and haplotype information in genome-wide association studies and downstream analyses can improve the utility of genomics for individuals from diverse and recently admixed ancestries. However, most existing simulation, visualization and variant analysis frameworks are based on variant-level analysis and do not automatically handle these features. We present haptools, an open-source toolkit for performing local ancestry aware and haplotype-based analysis of complex traits. Haptools supports fast simulation of admixed genomes, visualization of admixture tracks, simulation of haplotype- and local ancestry-specific phenotype effects and a variety of file operations and statistics computed in a haplotype-aware manner.

Availability and implementation: Haptools is freely available at https://github.com/cast-genomics/haptools.

Documentation: Detailed documentation is available at https://haptools.readthedocs.io.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Example analyses performed using haptools. (a) An example karyogram depicting local ancestry tracts simulated by the simgenotype command. (b) Manhattan plot showing association summary statistics (−log10 P-values) for a trait with a single SNP (circled) simulated to be causal only when it occurs on an African haplotype. The SNP (rs12740374) is highly significant in simulated African but not European individuals. It has an intermediate P-value in a sample of simulated admixed individuals. (c) Manhattan plot showing association summary statistics for a trait simulated with either two causal SNPs (rs36046716 and rs1046282; left) or a single causal haplotype (composed of alleles from the two SNPs; right). Red = SNP-level P-values and orange = haplotype-level P-values for the variants of interest. When the haplotype is causal (right), it has a more significant P-value than the SNPs it is composed of. This large effect could be missed by variant-level association tests. Detailed methods underlying results shown in the figures are in the Supplementary Material.
See this image and copyright information in PMC

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