selscan: An Efficient Multithreaded Program to Perform EHH-Based Scans for Positive Selection

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.…

• AP
  Alfred P. Sloan Foundation
• NI
  National Institutes of Health

  Awards: P60MD006902, 1R01HL117004, UL1RR024131, 1R01HG007644