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

• call to discover and genotype structural variants
• merge structural variants across VCF/BCF files and within a single VCF/BCF file
• filter somatic or germline structural variants

Long-read SV calling

• lr for long-read SV discovery

Copy-number variant calling

• cnv to discover and genotype copy-number variants
• classify somatic or germline copy-number variants

Input

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.

Output

The output is available in BCF and VCF format. Additionally a log file is provided.

References

More information are available on GitHub.