HAP-SAMPLE2: data-based resampling for association studies with admixture

TL;DR

HAP-SAMPLE2 is a tool for simulating genetic data that handles admixture and rare variants, useful for large-scale genetic studies.

Contribution

It introduces features for population admixture and rare variant analysis in genotype-phenotype simulations.

Findings

HAP-SAMPLE2 supports the simulation of admixed populations and rare variants with customizable parameters.

The tool enables efficient creation of complex datasets for projects like the 1000 Genomes Project.

It includes burden testing for rare variants using multiple weighting schemes.

Abstract

HAP-SAMPLE2 extends the functionality of the original HAP-SAMPLE tool for simulating genotype-phenotype data, now with features to handle population admixture and rare variant analysis. It allows users to define parameters such as disease prevalence and allele effect sizes for both common and rare variant simulations.

HAP-SAMPLE2 provides an efficient means for simulating complex datasets, suitable for large-scale projects like the 1000 Genomes Project. Its capabilities for population admixture allow users to create admixed populations or preserve substructures while introducing novel variation through artificial recombination. Additionally, the tool supports burden testing for rare variants using fixed and Madsen-Browning weighting schemes.

The software, along with a detailed vignette, is available on GitHub: https://github.com/M3dical/HAPSAMPLE2.

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