LocalNgsRelate

LocalNgsRelate infers identity-by-descent (IBD) sharing along the genome between pairs of individuals from low-depth next-generation sequencing (NGS) data by using genotype likelihoods to account for genotype uncertainty.

Key Features:

• Probabilistic approach: Uses genotype likelihoods rather than called genotypes to incorporate uncertainty from low-depth NGS data.
• Improved accuracy: Demonstrated higher accuracy for IBD inference compared to genotype-based methods such as Albrechtsen et al. (2009) and hap-IBD.
• Low-depth performance: Operates effectively on NGS data with depths as low as 2×.

Scientific Applications:

• Population genetics: Detects shared ancestry and relatedness patterns in population-genetic studies using low-depth NGS.
• Ancestry inference: Identifies IBD segments to support inference of recent shared ancestry between individuals.
• Shared genomic segment discovery: Locates shared genomic segments (IBD tracts) among individuals from low-depth sequencing data.

Methodology:

Infers IBD sharing by leveraging genotype likelihoods to model and incorporate genotype-call uncertainty instead of relying on called genotypes.