Haptools: a toolkit for admixture and haplotype analysis.
Bioinformatics
; 39(3)2023 03 01.
Article
in En
| MEDLINE
| ID: mdl-36847450
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.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Software
/
Genome-Wide Association Study
Language:
En
Journal:
Bioinformatics
Journal subject:
INFORMATICA MEDICA
Year:
2023
Type:
Article
Affiliation country:
United States