Related Experiment Video
Updated: Aug 8, 2025
Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
Published on: December 13, 2024
Haptools: a toolkit for admixture and haplotype analysis
Arya R Massarat1, Michael Lamkin2, Ciara Reeve3
1Bioinformatics and Systems Biology Graduate Program, Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.
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.
