WHAMM!: Whole-Genome Homozygosity Analysis and Mapping Machina
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 Research (CHGR), Massachusetts General Hospital (MGH), and the Broad Institute of Harvard & MIT, with help, data, and testing provided by a host of folks.  

 

Quick links

BF Voight's Home page

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