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DELLY specifications

Information


Unique identifier OMICS_00313
Name DELLY
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.7.9
Stability Stable
Maintained Yes

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Documentation


Publication for DELLY

DELLY citations

 (74)
call_split

Compound heterozygous TYK2 mutations underlie primary immunodeficiency with T cell lymphopenia

2018
Sci Rep
PMCID: 5934390
PMID: 29725107
DOI: 10.1038/s41598-018-25260-8
call_split See protocol

[…] oftware.broadinstitute.org/gatk/), followed by data annotation using the Illumina VariantStudio software. Analyses of the SVs from the exome sequencing data were performed using the programs, Pindel, Delly and gridss (https://github.com/PapenfussLab/gridss), at their default settings. For Sanger DNA sequencing, coding regions of the TYK2 gene were amplified from the synthesized cDNA using the foll […]

library_books

Novel sequences, structural variations and gene presence variations of Asian cultivated rice

2018
Sci Data
PMCID: 5931083
PMID: 29718005
DOI: 10.1038/sdata.2018.79

[…] SV data obtained by calling against the Nipponbare reference genome using novoBreak because it had the lowest false positive rate when compared with results from several tools such as BreakDancer and Delly. This SV data set contains a total number of 93,683 SVs (deletions, inversions and duplications of >100 bps and <1 Mbps, and translocations), or an average of 12,178 SVs per genome detected in t […]

library_books

FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods

2018
Genome Biol
PMCID: 5859555
PMID: 29559002
DOI: 10.1186/s13059-018-1404-6

[…] he 1000GP Phase 3 SV callset [, , ]. For Jaccard similarity, FusorSV outperformed all individual algorithms (40%) with MetaSV as the next best method (32%), followed by BreakDancer, BreakSeq2, LUMPY, DELLY, and Hydra (all near 20%).Fig. 4For duplication calls, GenomeSTRiP performed at 26% precision and 14% recall, while CNVnator performed at 22% precision and 3% recall. The MetaSV duplication call […]

library_books

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

2018
Nat Commun
PMCID: 5826927
PMID: 29483503
DOI: 10.1038/s41467-018-03273-1

[…] nce genome (e.g., Barnacle and Dissect, which are RNA-Seq analysis tools that can also be used to analyze genomic data). There are also several tools that employ a combination of these (e.g., Pindel, Delly, novoBreak, and GASVPro), which, unfortunately, only consider uniquely mapped reads and cannot identify alterations in repetitive DNA. In fact, no available tool, even those designed to identify […]

library_books

A recurrent kinase domain mutation in PRKCA defines chordoid glioma of the third ventricle

2018
Nat Commun
PMCID: 5824822
PMID: 29476136
DOI: 10.1038/s41467-018-02826-8

[…] ng htslib 1.1), Picard tools: 1.97 (1504), GATK: Appistry v2015.1.1–3.4.46–0-ga8e1d99, CNVkit: 0.7.2, Pindel: 0.2.5b8, SATK: Appistry v2015.1.1–1-gea45d62, Annovar: v2016Feb01, Freebayes: 0.9.20, and Delly: 0.7.2–. Single nucleotide variants and insertions/deletions were visualized and verified using Integrated Genome Viewer. Genome-wide copy number analysis based on on-target and off-target reads […]

library_books

Actionable perturbations of damage responses by TCL1/ATM and epigenetic lesions form the basis of T PLL

2018
Nat Commun
PMCID: 5814445
PMID: 29449575
DOI: 10.1038/s41467-017-02688-6

[…] the same caller (‘Published validation rates of calls made by previous versions of MuTect in coding region’).We inferred structural variations by mapping distance and order of paired-end reads using DELLY (version 0.7.2) and filtered for a minimum genotype quality of 200, for no LowQual entries, minimum depth of 5 reads, and for split-read support (more precise breakpoint localization). For struc […]

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DELLY institution(s)
European Molecular Biology Laboratory (EMBL), Genome Biology, Heidelberg, Germany; EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK; European Molecular Biology Laboratory (EMBL), Core Facilities and Services, Heidelberg, Germany
DELLY funding source(s)
Supported by The European Commission (i.e. the EurocanPlatform project, Health-F2-2010-260791), the German Cancer Aid (109252) and the BMBF (ICGC ‘PedBrain’ Tumor Project, 01KU1201C).

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