WHAMM!: Whole-Genome Homozygosity Analysis and Mapping Machina WHAMM...!
Latest WHAMM release is v0.14 (03-Nov-2008)

Whole-Genome Homozygosity Analysis and Mapping Machina

Introduction | Basics | Download | Commands | Usage | Input | Output | Association | Summaries | Permutations | Imputations | FAQ

1. Introduction

2. Basic information

3. Download and general notes

4. Command reference table

5. The Model, Usage, and Pipeline 6. Input Files and Formats 7. Output Files and Formats 8. Association Analysis 9. Data Summaries 10. Permutations 11. Integrated Haplotype Score (iHS) Selection Scan 12. Note on Imputated Data

XX. FAQ & Hints


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


  • Operates on Phased and unphased genotyped data
  • Estimates relavent population genetic parameters of interest (frequency and tract lengths of homozygous segements)
  • Performs association analysis between homozygosity at specific genomic locale on quantitative trait and dichotomous outcomes
  • Easy extraction and identification of homozygous regions of interest, and those individuals who are homozygous, and population haplotype frequency estimates
  • Relatively speedy and efficient implementation

This document last modified Monday, 02-Apr-2012 17:35:45 EDT