Zachary A Szpiech, Ryan D Hernandez
(Submitted on 26 Mar 2014)
Haplotype-based scans to detect natural selection are useful to identify recent or ongoing positive selection in genomes. As both real and simulated genomic datasets grow larger, spanning thousands of samples and millions of markers, there is a need for a fast and efficient implementation of these scans for general use. Here we present selscan, an efficient multi-threaded application that implements Extended Haplotype Homozygosity (EHH), Integrated Haplotype Score (iHS), and Cross-population Extended Haplotype Homozygosity (XPEHH). selscan performs extremely well on both simulated and real data and over an order of magnitude faster than existing available implementations. It calculates iHS on chromosome 22 (22,147 loci) across 204 CEU haplotypes in 502s on one thread (77s on 16 threads) and calculates XPEHH for the same data relative to 210 YRI haplotypes in 907s on one thread (107s on 16 threads). Source code and binaries (Windows, OSX and Linux) are available at this https URL.