Dataset Information

Modelling haplotypes with respect to reference cohort variation graphs.

ABSTRACT:

Motivation

Current statistical models of haplotypes are limited to panels of haplotypes whose genetic variation can be represented by arrays of values at linearly ordered bi- or multiallelic loci. These methods cannot model structural variants or variants that nest or overlap.

Results

A variation graph is a mathematical structure that can encode arbitrarily complex genetic variation. We present the first haplotype model that operates on a variation graph-embedded population reference cohort. We describe an algorithm to calculate the likelihood that a haplotype arose from this cohort through recombinations and demonstrate time complexity linear in haplotype length and sublinear in population size. We furthermore demonstrate a method of rapidly calculating likelihoods for related haplotypes. We describe mathematical extensions to allow modelling of mutations. This work is an important incremental step for clinical genomics and genetic epidemiology since it is the first haplotype model which can represent all sorts of variation in the population.

Availability and implementation

Available on GitHub at https://github.com/yoheirosen/vg .

Contact

benedict@soe.ucsc.edu.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Rosen Y

PROVIDER: S-EPMC5870562 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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Publications

Modelling haplotypes with respect to reference cohort variation graphs.

Rosen Yohei Y Eizenga Jordan J Paten Benedict B

Bioinformatics (Oxford, England) 20170701 14

<h4>Motivation</h4>Current statistical models of haplotypes are limited to panels of haplotypes whose genetic variation can be represented by arrays of values at linearly ordered bi- or multiallelic loci. These methods cannot model structural variants or variants that nest or overlap.<h4>Results</h4>A variation graph is a mathematical structure that can encode arbitrarily complex genetic variation. We present the first haplotype model that operates on a variation graph-embedded population refere ...[more]

PMID: 28881971

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Dataset Information

Modelling haplotypes with respect to reference cohort variation graphs.

Motivation

Results

Availability and implementation

Contact

Supplementary information

Publications

Modelling haplotypes with respect to reference cohort variation graphs.

Similar Datasets

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