Integrated Haplotype Score calculator

eagle-i ID

Resource Type

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++