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 rela

SUBMITTER: Rosen Y 

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

REPOSITORIES: biostudies-literature