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Haplotype-based scans to detect natural selection are useful to identifyrecent or ongoing positive selection in genomes. As both real and simulatedgenomic datasets grow larger, spanning thousands of samples and millions ofmarkers, there is a need for a fast and efficient implementation of these scansfor general use. Here we present selscan, an efficient multi-threadedapplication that implements Extended Haplotype Homozygosity (EHH), IntegratedHaplotype Score (iHS), and Cross-population Extended Haplotype Homozygosity(XPEHH). selscan accepts phased genotypes in multiple formats, including TPED,and performs extremely well on both simulated and real data and over an orderof magnitude faster than existing available implementations. It calculates iHSon chromosome 22 (22,147 loci) across 204 CEU haplotypes in 353s on one thread(33s on 16 threads) and calculates XPEHH for the same data relative to 210 YRIhaplotypes in 578s on one thread (52s on 16 threads). Source code and binaries(Windows, OSX and Linux) are available at https://github.com/szpiech/selscan .

Selscan: an efficient multi-threaded program to perform EHH-based scans for positive selection