selscan

selscan implements haplotype-based scans to detect recent or ongoing positive selection in genomic datasets.

Key Features:

• Implemented statistics: Computes Extended Haplotype Homozygosity (EHH), Integrated Haplotype Score (iHS), and Cross-population EHH (XPEHH).
• Multithreaded performance: Uses multithreading to accelerate computation on large simulated and real datasets.
• Input formats: Accepts phased genotypes in formats including TPED.
• Performance benchmarks: iHS on chromosome 22 (22,147 loci) with 204 CEU haplotypes: 353 seconds (1 thread) and 33 seconds (16 threads); XPEHH relative to 210 YRI haplotypes: 578 seconds (1 thread) and 52 seconds (16 threads).
• Scalability: Designed to process extensive genomic datasets efficiently for high-throughput analyses.

Scientific Applications:

• Detection of positive selection: Identifies loci with extended haplotypes indicative of recent or ongoing selective sweeps within populations.
• Comparative population genomics: Detects differential selection between populations by comparing haplotype homozygosity.
• Evolutionary biology and population genetics: Supports inference of adaptive traits and evolutionary pressures from large-scale genotype data.

Methodology:

Implements EHH, iHS, and XPEHH: EHH measures decay of haplotype homozygosity with distance from a focal SNP; iHS quantifies integrated haplotype homozygosity within a population; XPEHH compares haplotype homozygosity between populations.