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Delly filter (version 0.9.1+galaxy1)
Generic options
Generic options 0
SV calling options
SV calling options 0
Output options
Output options 0

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.