Delly2

Delly2 detects and genotypes structural variants (deletions, tandem duplications, inversions, translocations and complex rearrangements) from short-read massively parallel sequencing to characterize genomic rearrangements at single-nucleotide resolution.

Key Features:

• High sensitivity and specificity: Detects structural variants with high sensitivity and specificity across varied sequencing parameters.
• Integrated evidence model: Integrates short-insert paired-end reads, long-range mate-pairs, and split-read alignments to identify simple and complex rearrangements.
• Single-nucleotide resolution: Pinpoints breakpoints at single-nucleotide resolution for precise variant characterization.
• Comprehensive detection: Detects copy-number variable deletions and tandem duplications, balanced rearrangements such as inversions and reciprocal translocations, and complex structural events.
• Validation and performance: Performance evaluated on simulated datasets and applied to 1000 Genomes Project data and cancer genomes with validation confirming high specificity for deletions.
• Visualization tools: Provides visualization utilities including Delly-maze and Delly-suave.

Scientific Applications:

• Population genomics: Characterizing genetic diversity and structural variation in population-scale datasets such as the 1000 Genomes Project.
• Cancer genomics: Detecting and genotyping somatic rearrangements in tumor genomes.
• Personalized medicine: Informing disease etiology and potential therapeutic targets through precise SV characterization.
• Mechanistic studies: Investigating formation mechanisms and functional consequences of structural variants.

Methodology:

Combines short-insert paired-end reads, long-range mate-pair evidence and split-read alignments to detect and genotype deletions, tandem duplications, inversions, translocations and complex SVs at single-nucleotide resolution, with performance assessed on simulated datasets and applied to 1000 Genomes Project and cancer genome data.