SNP Haplotyping and Linkage Disequilibrium Mapping using Models of Haplotype Block Variation

HaploBlock is a software program which provides an integrated approach to haplotype block identification, haplotyping SNPs (or haplotype phasing, resolution or reconstruction) and linkage disequilibrium (LD) mapping (or genetic association studies). HaploBlock is suitable for high density haplotype or genotype SNP marker data and is based on a statistical model which takes account of recombination hotspots, bottlenecks, genetic drift and mutations and has a Markov Chain at its core.
The HaploBlock program includes many tools related to SNP data and haplotype blocks, including:

  • Inferring haplotype block models from phased or unphased data.
  • Haplotype resolution using haplotype block models.
  • LD mapping for haplotype or genotype data using block models.
  • Simulating a population descended from a bottleneck event.
  • Haplotype resolution by the Clark algorithm or Local EM.
  • Measuring the quality of a haplotype resolution.

A full list with explanations can be found in the Instruction Manual.

Download version 1.2, which adds LD mapping functions and other improvements detailed in the Instruction Manual.

The LD Mapping Supplement explains how HaploBlock performs high resolution block-based LD mapping.

The Bayesian Network statistical model upon which HaploBlock is based was jointly developed by Dan Geiger and Gideon Greenspan. The software and documentation were written by Gideon Greenspan, to whom any comments or bug reports should be directed.
Information and data sources:
  • GeneStat portal for statistical genetics.
  • HapMap international haplotype mapping project for the entire human genome.
  • Chromosome 21 haplotype block tables at Perlegen.
  • 5q31 haplotype data at The Broad Institute.
Other software relating to haplotype block partitioning, haplotype phasing or haplotype mapping:
  • MDLBlockFinder and MDBlocks also use statistical models for haplotype block identification.
  • DMLE and BLADE software for high-resolution LD mapping.
  • PHASE software for haplotype resolution.
  • HAPLOTYPER and PL-EM divide-and-conquer methods for haplotype resolution.
  • HAP software for haplotype resolution using imperfect phylogeny.
  • Gerbil software for phasing and block partitioning genotypes.
  • HaploBlockFinder, HapBlock and htSNPer software for block partitioning and tag SNP selection.