Skip to main content
Download PDF
- Main
Modelling haplotypes with respect to reference cohort variation graphs
Published Web Location
https://doi.org/10.1093/bioinformatics/btx236Abstract
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.Many UC-authored scholarly publications are freely available on this site because of the UC's open access policies. Let us know how this access is important for you.
Main Content
For improved accessibility of PDF content, download the file to your device.
Enter the password to open this PDF file:
File name:
-
File size:
-
Title:
-
Author:
-
Subject:
-
Keywords:
-
Creation Date:
-
Modification Date:
-
Creator:
-
PDF Producer:
-
PDF Version:
-
Page Count:
-
Page Size:
-
Fast Web View:
-
Preparing document for printing…
0%