Haplotype-based association analysis package

Shaun Purcell, Massachusetts General Hospital, Boston, MA, USA
Pak Sham, Hong Kong University, Hong Kong
Conditional test tutorial
Future developments

whap package is superseded by PLINK

This package is no longer supported. The majority of the functionality for conditional haplotype tests in population-based samples has been implemented in PLINK, with a better interface and more robust, faster computation: please use that from now on.



whap provides a method for testing SNP haplotype associations with qualitative and quantitative traits in samples of individuals with or without parental genotype data.

You are advised to look at the examples first, then read all the instructions and follow the more advanced tutorial, and especially the warnings in order to avoid common problems.

What whap can do
  • Analyse quantitative and qualitative traits
  • Handle unrelated individuals and/or parent-offspring trio data
  • Perform a regression-based haplotype association test for SNP data
  • Perform a secondary test based on pairwise haplotype similarity
  • Phase genotype data using a standard E-M approach, and handle ambiguity in E-M inferred haplotypes
  • Include covariates and moderator variables
  • Flexibly constrain effects across haplotypes to tested nested models
  • Perform a robust within-family test when parental genotypes are present
  • Analyse multiallelic markers (new)
  • Use dominant or recessive (new) genetic models (new)
What whap can't do
  • Analyze the whole genome (see the PLINK package for this)
  • Determine or use information on haplotype block structure
  • Handle multiple siblings or larger families
  • Spot errors in a user-friendly fashion...
    Purcell S, Daly MJ & Sham PC (2007) WHAP: haplotype-based 
      association analysis. Bioinformatics, 23(2):255-256.

Created by Shaun Purcell; Last updated by Lori Thomas: March 2006