FLARE

FLARE estimates local ancestry at each genomic position in admixed individuals to identify ancestral sources for population genetics and admixture mapping.

Key Features:

• High Accuracy: Uses an extended Li and Stephens model to improve accuracy of local ancestry inference.
• Computational Efficiency: Incorporates computational techniques developed for genotype imputation to process large-scale genomic data efficiently.
• Memory Optimization: Performs on-the-fly compression of reference haplotypes and uses stored checkpoints to reduce memory requirements.
• Scalability: Employs composite reference haplotypes to reduce computation time and scale to datasets with hundreds of thousands of sequenced individuals.

Scientific Applications:

• Admixture Mapping: Provides local ancestry calls that enable identification of genomic regions associated with traits or diseases that differ across ancestral populations.
• Population Genetic Analyses: Facilitates studies of complex genetic architectures and evolutionary histories in admixed populations.

Methodology:

Combines an extended Li and Stephens model with computational strategies from genotype imputation, including on-the-fly compression of reference haplotypes, stored checkpoints, and composite reference haplotypes.