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Table 2 Summary of selected software available for whole-genome haplotyping

From: Whole-genome haplotyping approaches and genomic medicine

Method

Software

Summary

Reference(s)

Molecular - haplotype assembly

HapCut (OSS)

A combinatorial approach implementing a max-cut-based algorithm and optimized minimum error correction (MEC) solution

[22]

Single Individual Haplotyper (OSS)

A collection of algorithms including RefHap, a heuristic algorithm for sorting reads into haplotype bins

[31],[37]

H-BOP (OSS)

Heuristic algorithm for optimizing a combination of the MEC and Maximum Fragments Cut models

[38]

MixSIH (OSS)

Probabilistic mixture model

[39]

HASH (OSS)

Markov chain Monte Carlo algorithm

[21]

Genetic analysis

Haploscribe (OSS)

Implements a parsimony approach to generate inheritance state vectors and a hidden Markov model to deduce haplotypes

[8]

Population inference

Beagle (OSS)

Phased input data are used to build a local haplotype cluster model, which is sampled using a hidden Markov model. Iterations and the Viterbi algorithm are used to select the `most likely haplotype

[40]

fastPHASE (OSS)

Enhancement of PHASE. Implements a haplotype-clustering model with a fixed number of clusters and hidden Markov model assumptions for cluster membership. Expectation-maximization methods are incorporated for parameterization

[41]

GERMLINE (OSS)

Implements a hashing-algorithm approach to identifying whole-haplotype segment sharing

[42]

IMPUTE2

Pre-phasing, imputation and haplotype sampling strategy incorporating a Monte Carlo algorithm and Markov model calculations

[43]

MaCH

Implements a Markov Chain algorithm for genotype imputation and haplotyping

[44]

PHASE (OSS)

Implements Bayesian haplotype reconstruction

[45]

SHAPEIT

Implements hidden Markov model sampling

[46],[47]

SNPTools (OSS)

A population imputation pipeline that generates genotype likelihoods using a binary sequence map-specific binomial mixture model. Haplotypes are then sampled using a hidden Markov model

[48]

WinHAP (OSS)

Scalable sliding windows are used to optimize haplotypes and a parsimony approach iteratively restricts the number of solutions

[49]

Combination strategies

HARSH (OSS)

Sampling within a probabilistic model combining read data with a reference panel of haplotypes. Successor to Hap-SeqX

[50]

SHAPEIT2

Adds short-read molecular information to population inference

[51]

Prism

Combines haplotype assembly and population inference

[36]

PPHS

Implements a phylogeny model to estimate haplotype frequencies recursively using the expectation maximization algorithm

[52]

 

FamilyQuartet (OSS)

Integrates physical, genetic and population phasing

[53]

  1. Abbreviations: OSS open source software, MEC minimum error correction.