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

Delly classify for somatic or germline copy-number variants.

Input

Delly classify requires an input file in BCF format that can be generated with e.g. Delly merge. Additionally a tab-delimited sample description file is required where the first column is the sample id (as in the VCF/BCF file) and the second column is either tumor or control.

Output

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

References

More information are available on GitHub.