Whole-genome Association Mapping Machina

eagle-i ID

Resource Type

Properties

1. Uses algorithmic software component

   Integrated Haplotype Score calculator

2. Resource Description

   "WHAMM is a free, open-source analysis package designed to estimate patterns of homozygosity in whole genome data sets, as well as perform a range of association analyses and summaries on the resultant output. Additional functionality will be added to also scan whole-genome platform data for signatures of extended haplotype homozygosity consistent with positive selection, summarized with the integrated Haplotype Score (iHS), though this functionality remains to be implemented."

3. Additional Name

   WHAMM

4. Used by

   Voight Laboratory

5. Version

   0.14a

6. Operating System

   Linux

7. Operating System

   Unix

8. Data Input

   Phased genotype data

9. Data Input

   Unphased genotype data

10. Data Input

    Marker map

11. Data Input

    Sample information

12. Data Input

    Phenotype data

13. Data Input

    Phased data loader

14. Data Input

    Keeplist

15. Data Output

    Log

16. Data Output

    Segment map

17. Data Output

    Haplotype frequencies

18. Data Output

    Homozygosity probabilities

19. Data Output

    Forward/Backward painting

20. Data Output

    Estimated homozygosity parameters

21. Data Output

    Homozygosity dosage file

22. Data Output

    Sample listings

23. Data Output

    Basic association results

24. Data Output

    Regression association results

25. Software purpose

    Population genetics analysis objective

26. Website(s)

    http://coruscant.itmat.upenn.edu/whamm/index.html

27. Developed by

    Voight, Benjamin F., PhD

28. Algorithm used

    Fischer's Exact Test

29. Coded in

    Perl