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Integrated Haplotype Score calculator

eagle-i ID

http://eagle-i.itmat.upenn.edu/i/0000013d-4166-3ff6-ae62-bb6880000000

Resource Type

  1. Algorithmic software component

Properties

  1. Resource Description
    "This program is designed to calculate the integrated Hapotype Score (iHS), described in Voight and Kudaravelli et al. (PLoS Biology, 2006). This tool modifies slightly upon that program found elsewhere, reporting scores of all SNPs with error codes." "The integrated haplotype Score (iHS) is a measure of the amount of extended haplotype homozygosity (EHH) at a given SNP along the ancestral allele relative to the derived allele. This measure is typically standardized (mean 0, variance 1) empirically to the distribution of observed iHS scores over a range SNPs with similar derived allele frequencies. Extended homozygosity for haplotypes on a high frequency derived allele relative to the ancestral background is a signature of a positively selected sweep which has not yet reached fixation. A classic signature is in the lactase region (LCT), where presumably selection on lactase-persistence into adulthood is a trait that has be subject to a selective sweep in European (and some African populations) which has not fixed completely."
  2. Additional Name
    iHS calculator
  3. Used by
    Voight Laboratory
  4. Version
    1.0.1
  5. Operating System
    Linux
  6. Operating System
    Unix
  7. Data Input
    Marker map information
  8. Data Input
    Phased haplotype data
  9. Data Output
    Integrated haplotype scores for SNPs
  10. Software purpose
    Population genetics analysis objective
  11. Related Publication or Documentation
    A map of recent positive selection in the human genome
  12. Website(s)
    http://coruscant.itmat.upenn.edu/software.html
  13. Website(s)
    http://coruscant.itmat.upenn.edu/whamm/ihs.html#scan
  14. Developed by
    Voight, Benjamin F., Ph.D.
  15. Coded in
    C++
 
RDFRDF
 
Provenance Metadata About This Resource Record
  1. workflow state
    Published
  2. contributor
    fcoldren
  3. created
    2013-03-06T15:34:37.021-05:00
  4. creator
    fcoldren
  5. modified
    2013-03-15T13:59:56.841-04:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016