selscan: An Efficient Multithreaded Program to Perform EHH-Based Scans for Positive Selection
By Zachary A. Szpiech, Ryan D. Hernandez. Molecular biology and evolution, 2014
737 citations recorded by the source corpus.
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.
Subfields: Genetics
View Paper: https://www.semanticscholar.org/paper/8cc32c3f68a7309b33de0602e9d56721703e50ea
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In Genetics
Citations in the corpus
- A method for genome-wide genealogy estimation for thousands of samples (2019, methodology): “We use selscan [13] and hapbin [14] to calculate iHS scores.”
- rehh 2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure (2016, methodology): “This stimulated the development of alternative R-free solutions (Szpiech & Hernandez, 2014; Maclean et al , 2015).”