Mapping to a Reference Genome Structure

Benedict Paten; Adam Novak; David Haussler

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arXiv · 1404.5010

Mapping to a Reference Genome Structure

Benedict Paten·Adam Novak·David Haussler

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Abstract

To support comparative genomics, population genetics, and medical genetics, we propose that a reference genome should come with a scheme for mapping each base in any DNA string to a position in that reference genome. We refer to a collection of one or more reference genomes and a scheme for mapping to their positions as a reference structure. Here we describe the desirable properties of reference structures and give examples. To account for natural genetic variation, we consider the more general case in which a reference genome is represented by a graph rather than a set of phased chromosomes; the latter is treated as a special case.

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Benedict Paten, Adam Novak, David Haussler. 2014-04-20. Mapping to a Reference Genome Structure. https://arxiv.org/abs/1404.5010

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