DELLY: structural variant discovery by integrated paired-end and split-read analysis

By Tobias Rausch, T. Zichner, A. Schlattl, A. Stütz, Vladimir Benes, Jan O. Korbel. Bioinform., 2012

2,205 citations recorded by the source corpus.

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

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0b039e448c10302ac0d0b0ed4629c8ac490ae0a8

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Citations in the corpus

SpeedSeq: Ultra-fast personal genome analysis and interpretation (2014, methodology): “3 hours of processing time for two other leading SV detection tools, DELLY[26] and GASVPRO[27].”
LUMPY: a probabilistic framework for structural variant discovery (2012, methodology): “In contrast, although other tools such as GASVPro [4], DELLY [3], CNVer [7], CREST [6] and Genome STRiP [5] also exploit multiple SV detection signals, to our knowledge they first use one signal (that is, read-pair) to drive discovery and then refine and/or genotype candidates with a second signal (”
Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing (2019, neutral): “…highlights a subset of algorithms that can call many SVs with a high level of precision and re-call for both simulated and real datasets, which include 1-2-3-SV [39], DELLY [32], GRIDSS [40], inGAP-sv [41], Lumpy [35], Manta [42], MetaSV [43], Pindel [34], SoftSV [44], SvABA [45], and Wham [46].”