Haplotype phase inference software tools | Population genomics

Two categories of computational methods exist for determining haplotypes: haplotype phasing and haplotype assembly. Given the genotypes of a sample of individuals from a population, haplotype phasing attempts to infer the haplotypes of the sample…

Two categories of computational methods exist for determining haplotypes: haplotype phasing and haplotype assembly. Given the genotypes of a sample of individuals from a population, haplotype phasing attempts to infer the haplotypes of the sample using haplotype sharing information within the sample. In the related problem of genotype imputation, a phased reference panel is used to infer missing markers and haplotype phase of the sample (Marchini and Howie, 2010). Methods for haplotype phasing and imputation are based on computational (Halldórsson et al., 2004) and statistical inference (Browning and Browning, 2011) techniques, but both use the fact that closely spaced markers tend to be in linkage disequilibrium and smaller haplotypes blocks are often shared in a population of seemingly unrelated individuals. Source text: Aguiar and Istrail, 2012.

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Estimates haplotype phase either within a genotyped cohort or using a phased…

Estimates haplotype phase either within a genotyped cohort or using a phased reference panel. A phasing algorithm attaining high accuracy across a broad range of cohort sizes by efficiently…

It can resolve long haplotypes or infer missing genotypes in samples of…

It can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals. Specifically, MACH can estimate haplotypes, impute missing genotypes in a variety of populations, using…

A state of the art software package for analysis of large-scale genetic data…

A state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples.

Provides a fast program for haplotype-aware consequence calling which can take…

Provides a fast program for haplotype-aware consequence calling which can take into account known phase. BCFtools/csq is part of the BCFtools package. Applied to the 1000 Genomes Project data,…

Reconstructs local tree topologies for a set of population single-nucleotide…

Reconstructs local tree topologies for a set of population single-nucleotide polymorphism (SNP) haplotypes undergoing recombination. Due to recombination, tree topologies change as one moves accross…

An algorithm that models linkage disequilibrium using a simple multivariate…

An algorithm that models linkage disequilibrium using a simple multivariate Gaussian distribution. The key feature of our algorithm is its speed. MarViN is hundreds of times faster than other methods…

An efficient method that combines multi-SNP read information with reference…

An efficient method that combines multi-SNP read information with reference panels of haplotypes for improved genotype and haplotype inference in sequencing data. Unlike previous phasing methods that…

Allows users to perform haplotype phasing and local ancestry inference (LAI).…

Allows users to perform haplotype phasing and local ancestry inference (LAI). Loter is a python package that supplies a parameter-free and rapid software without specifications of statistical or…

A program to improve haplotype reconstruction using paired-end short reads.…

A program to improve haplotype reconstruction using paired-end short reads. Assuming that the users have run an existing phaser, HI processes the paired-end information in the raw data to form blocks…

A statistical haplotype reconstruction algorithm targeted for large-scale…

A statistical haplotype reconstruction algorithm targeted for large-scale disease association studies. HaploRec is especially suitable for data sets with a large number of subjects and a large number…

A fast haplotype phasing algorithm based on scalable sliding windows and…

A fast haplotype phasing algorithm based on scalable sliding windows and parsimony principle, which not only maintains the similar speed with the 2SNP but also has a much higher accuracy. In the…

An algorithm for haplotype resolution and block partitioning. The algorithm…

An algorithm for haplotype resolution and block partitioning. The algorithm uses a stochastic model for genotype generation, based on the biological finding that genotypes can be partitioned into…

Allows a rapid and accurate inference of haplotypes from population genotype…

Allows a rapid and accurate inference of haplotypes from population genotype data. ISHAPE first uses a rapid bootstrap step of iterative EM (IEM) haplotyping in randomly chosen samples of the…

A method for inferring haplotypes from sequence data utilizing information from…

A method for inferring haplotypes from sequence data utilizing information from both the reads and a reference dataset. Hap-seqX significantly improves current state of the art methods such as IMPUTE…

A program for haplotype inference, based on the maximum parsimony principle and…

A program for haplotype inference, based on the maximum parsimony principle and the collapse rule, a generalization of the well-known Clark's rule introduced by the authors. The performance of…

A tool for imputation of unobserved genotypes using a set of reference…

A tool for imputation of unobserved genotypes using a set of reference haplotype panel at a higher-density SNP set such as HapMap, and lower-density genotypes of a target individual using such as…

Determines the haplotypes of each person from unphased high-throughput…

Determines the haplotypes of each person from unphased high-throughput genotypes in family pedigrees. GenomeLaser features high accuracy, chromosome-range phasing distance, linear computing, flexible…

Implements a phasing algorithm, which is very fast and scalable. Haplotypes for…

Implements a phasing algorithm, which is very fast and scalable. Haplotypes for each genotype are inferred based on the maximum spanning tree of a graph with vertices corresponding to heterozygous…