DELLY: Structural Variant Discovery by Integrated Paired-end and Split-read Analysis

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2012 Sep 11

PMID 22962449

Citations 1153

Authors

Tobias Rausch

Thomas Zichner

Andreas Schlattl

Adrian M Stutz

Vladimir Benes

Jan O Korbel

Affiliations

Soon will be listed here.

Abstract

Motivation: The discovery of genomic structural variants (SVs) at high sensitivity and specificity is an essential requirement for characterizing naturally occurring variation and for understanding pathological somatic rearrangements in personal genome sequencing data. Of particular interest are integrated methods that accurately identify simple and complex rearrangements in heterogeneous sequencing datasets at single-nucleotide resolution, as an optimal basis for investigating the formation mechanisms and functional consequences of SVs.

Results: We have developed an SV discovery method, called DELLY, that integrates short insert paired-ends, long-range mate-pairs and split-read alignments to accurately delineate genomic rearrangements at single-nucleotide resolution. DELLY is suitable for detecting copy-number variable deletion and tandem duplication events as well as balanced rearrangements such as inversions or reciprocal translocations. DELLY, thus, enables to ascertain the full spectrum of genomic rearrangements, including complex events. On simulated data, DELLY compares favorably to other SV prediction methods across a wide range of sequencing parameters. On real data, DELLY reliably uncovers SVs from the 1000 Genomes Project and cancer genomes, and validation experiments of randomly selected deletion loci show a high specificity.

Availability: DELLY is available at www.korbel.embl.de/software.html

Contact: tobias.rausch@embl.de.

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