1. Haptools: a toolkit for admixture and haplotype analysis
- Author
-
Massarat, Arya R, Lamkin, Michael, Reeve, Ciara, Williams, Amy L, D’Antonio, Matteo, and Gymrek, Melissa
- Subjects
Mathematical Sciences ,Biological Sciences ,Statistics ,Genetics ,Human Genome ,Haplotypes ,Software ,Genome-Wide Association Study ,Genomics ,Genome ,Information and Computing Sciences ,Bioinformatics ,Biological sciences ,Information and computing sciences ,Mathematical sciences - Abstract
SummaryLeveraging 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 implementationHaptools is freely available at https://github.com/cast-genomics/haptools.DocumentationDetailed documentation is available at https://haptools.readthedocs.io.Supplementary informationSupplementary data are available at Bioinformatics online.
- Published
- 2023