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Summary sheet

Main use-cases extended haplotype heterozygosity estimation and visualization
Authors Alexander Klassmann Mathieu Gautier Renaud Vitalis
Latest version 3.2.2
License GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
Website https://www.google.com
Code repository https://gitlab.com/oneoverx/rehh
Publication https://doi.org/10.1111/1755-0998.12634
Tutorial authors Karamoko Niaré
Tutorial date 12/11/2023

Purpose

This tool computes several metrics of positive selection signatures along the genome of an organism. These metrics include the Extended Haplotype Homozygosity (EHH), integrated EHH (IHH), site-specific EHH (EHHS), integrated EHHS (iES), integrated haplotype homozygosity score (iHS), ratio of EHHS (Rsb) and cross-population EHH (XP-EHH). EHH is defined as the probability that two randomly chosen chromosomes, carrying the core allele, are homozygous over a given surrounding chromosomal region. More details on the EHH can be found in the paper published by Sabeti et al. 2002. This istechnically a useful gemomic metrics in malaria, as the nature and length of shared haplotypes and EHH scores flanking an allele, such as a drug resistance mutation, show the ancestral relationship between mutants and how selective sweep survived recombinations over time.

Existing resources

  • This tutorial give details on how to run the functions

Citation

 @Article{,
    author = {Mathieu Gautier and Renaud Vitalis},
    title = {rehh: An R package to detect footprints of selection in
      genome-wide SNP data from haplotype structure},
    journal = {Bioinformatics},
    year = {2012},
    volume = {28},
    number = {8},
    pages = {1176-1177},
  }
  @Article{,
    author = {Mathieu Gautier and Alexander Klassmann and Renaud
      Vitalis},
    title = {rehh 2.0: a reimplementation of the R package rehh to
      detect positive selection from haplotype structure},
    journal = {Molecular Ecology Resources},
    year = {2017},
    volume = {17},
    number = {1},
    pages = {78-90},
    doi = {10.1111/1755-0998.12634},
  }
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