What it does
Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.
Short-read SV calling
Long-read SV calling
Copy-number variant calling
Somatic filtering requires a called SV input with at least one tumor sample and a matched control sample. In addition, a tab-delimited sample description needs to be provided, in which the first column holds the sample ids (as found in the VCF/BCF input) and the second column specifies either tumor or control.
Germline SV calling is done by sample for high-coverage genomes or in small batches for low-coverage genomes.
The output is available in BCF and VCF format. Additionally a log file is provided.
More information are available on GitHub.