DELLY: Structural variant discovery by integrated paired-end and split-read analysis

DELLY is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. The algorithm is described in:

DELLY: structural variant discovery by integrated paired-end and split-read analysis
Tobias Rausch; Thomas Zichner; Andreas Schlattl; Adrian M. Stütz; Vladimir Benes; Jan O. Korbel
Bioinformatics 2012 28: i333-i339

If you have any questions, comments, bug reports or suggestions feel free to email me
or subscribe to the DELLY mailing list.

- Tobias Rausch

Tobias Rausch Email


A new multi-sample DELLY version is now available on github !!!

There are two DELLY packages, one with statically linked binaries and one with the source code and compiling instructions. Please subscribe to delly-users for questions, updates or bug reports.
Previous versions can be downloaded in the version history below.


The DELLY package contains four methods to detect deletions, tandem duplications, inversions and translocations. There is a separate tool for each SV type: Each method has a default help screen with all the command line options. You can simply access it using the method's name, i.e. ./delly, without any additional command line options. Below are typical usage scenarios: DELLY produces two output files for deletion and tandem duplication calling. One file with the paired-end predictions and one file with the split-read predictions. The split-read predictions are always a subset of the paired-end predictions and the unique structural variant id is kept across the paired-end and split-read calls, so every split-read call can be uniquely linked to a paired-end call. To get a list of all candidate sturctural variants a simple grep for the summary line is sufficient, i.e. grep ">Deletion" del.txt.


Version History


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Author: Tobias Rausch
Last change: 26th November 2013
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