hapbin: An efficient program for performing haplotype based scans for positive selection in large genomic datasets

Abstract

These files contain genome-wide integrated haplotype scores (iHS) for each of the 26 populations in the phase 3 release of the 1000 genomes project. iHS were calculated using the hapbin program that can be downloaded from https://github.com/evotools/hapbin. The 1000 genomes phased haplotypes were obtained from mathgen.stats.ox.ac.uk/impute and hapbin was run with default parameters. The iHS are provided in two formats; BED and bedGraph. For each SNP the unstandardised iHS was calculated as ln(iHH1/iHH0) and these values normalised using hapbin’s default parameters. If the normalised iHS was negative the absolute value is reported and this is indicated by a 1 in the fourth column following the “:” of the BED format file. The bedGraph formatted data can be easily viewed along the genome at the UCSC genome browser by specifying the URL to the corresponding file at http://genome-euro.ucsc.edu/cgi-bin/hgCustom?clade=mammal&org=Human&db=hg37.