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.
WHAMM is implemented in
PERL, but utilizes routines from R (for regression and numerical
maximization). The portion of the machinery which utilizes phased
whole-genome data was designed with the idea that BEAGLE
is utilized, and will seemlessly integrate with file formats generated
by that program (of course, alternative phasing program can be
utilized, assuming file formatting is applied). The package is
currently designed for the UNIX/Linux operating environment.
WHAMM is a development
project by Benjamin F. Voight at the Center for Human Genetics
Massachusetts General Hospital (MGH), and the Broad Institute of Harvard & MIT,
with help, data, and testing provided by a
host of folks.