IBDseq

IBDseq detects segments of identity-by-descent (IBD) and homozygosity-by-descent (HBD) in unphased genetic sequence data to identify shared ancestry and assess genotype error patterns in high-density sequencing studies.

Key Features:

• Adaptation to sequence data: Handles high-density sequence data with variant densities, distinct allele frequency distributions, and genotype error profiles compared to SNP array data.
• Efficient analysis of large datasets: Scales to analyze datasets comprising thousands of individuals for large-scale genetic studies.
• Multi-allelic marker compatibility: Processes multi-allelic markers to accommodate diverse genomic variant types.
• Probabilistic IBD inference and LOD scoring: Estimates probabilities of observed genotypes under IBD and non-IBD models for each pair of individuals and computes LOD (logarithm of odds) scores to quantify IBD likelihood.
• Genotype error rate estimation (SEQERR): Includes the SEQERR method to estimate genotype error rates at low-frequency variants by comparing observed and expected homozygote and heterozygote rates within detected IBD segments.

Scientific Applications:

• High power and accuracy: Detects IBD segments with high power and accuracy, outperforming Beagle Refined IBD, PLINK, and GERMLINE under various parameter settings.
• Validation on real datasets: Demonstrated utility and validation using data from the UK10K and 1000 Genomes projects.

Methodology:

Computational steps include estimating genotype probabilities under IBD and non-IBD models per pair of individuals, computing LOD scores to quantify IBD, and applying the SEQERR approach that compares observed versus expected homozygote and heterozygote rates within detected IBD segments to estimate genotype error rates.