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 | ||
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 | ||
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] |