title: Making the difference: integrating structural variation detection tools.
abstract: From prokaryotes to eukaryotes, phenotypic variation, adaptation and speciation has been associated with structural variation between genomes of individuals within the same species. Many computer algorithms detecting such variations (callers) have recently been developed, spurred by the advent of the next-generation sequencing technology. Such callers mainly exploit split-read mapping or paired-end read mapping. However, as different callers are geared towards different types of structural variation, there is still no single caller that can be considered a community standard; instead, increasingly the various callers are combined in integrated pipelines. In this article, we review a wide range of callers, discuss challenges in the integration step and present a survey of pipelines used in population genomics studies. Based on our findings, we provide general recommendations on how to set-up such pipelines. Finally, we present an outlook on future challenges in structural variation detection.
authors.forename: Ke
authors.initials: K
authors.lastname: Lin
authors.forename: Sandra
authors.initials: S
authors.lastname: Smit
authors.forename: Guusje
authors.initials: G
authors.lastname: Bonnema
authors.forename: Gabino
authors.initials: G
authors.lastname: Sanchez-Perez
authors.forename: Dick
authors.initials: D
authors.lastname: de Ridder
mesh_terms: D003627:Data Interpretation, Statistical; D005828:Genetics, Population; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing
keywords: integrative pipelines; next generation sequencing; population genomics; structural variation detection