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

Delly cnv requires are a sample (BAM), a genome (FASTA) and a mappability map (FASTA), which is available here. Intervals (BED), scanning regions (BED) and a delly SV file for breakpoint refinement (BCF) can be provided optionally.

Output

CNV (BCF) and coverage (compressed tabular) files are created.

References

More information are available on GitHub.