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  • 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. 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 http://www.korbel.embl.de/software.html Herein, we report a new integrative approach, called DELLY, that combines short-range and long-range paired-end mapping and split-read analysis for the discovery-at single nucleotide resolution-of balanced and unbalanced forms of structural variation, i.e. deletions, tandem duplications, inversions and translocations, achieving high sensitivity and specificity throughout the genome and for SVs falling into a wide size spectrum.
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