selscan

Haplotype-based scans to detect natural selection are useful to identify recent
or ongoing positive selection in genomes. As both real and simulated genomic data
sets 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 multithreaded application that implements
Extended Haplotype Homozygosity (EHH), Integrated Haplotype Score (iHS), and
Cross-population EHH (XPEHH). selscan accepts phased genotypes in multiple
formats, including TPED, and 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 353 s on one thread (33 s on 16 threads) and calculates XPEHH for
the same data relative to 210 YRI haplotypes in 578 s on one thread (52 s on 16
threads). Source code and binaries (Windows, OSX, and Linux) are available at
https://github.com/szpiech/selscan.

selscan: an efficient multithreaded program to perform EHH-based scans for positive selection.

selscan is a tool to compute Extended Haplotype Homozygosity (EHH) based scans for positive selection in genomes. The selscan algorithm computes Integrated Haplotype Score (iHS), and Cross-population EHH (XPEHH). As input selscan can use phased genotypes in various
formats.

selscan

Topic

Detail

Publications

Download and documentation