DELLY protocols

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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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Publication for DELLY

DELLY in pipelines

 (17)
2018
PMCID: 5797622
PMID: 29441079
DOI: 10.3389/fpls.2018.00044

[…] and indels were detected using the snp analyses software gatk (mckenna et al., ). annovar software and the existing genomic annotation file (gff/gtf) were used to annotate the snps (wang et al., ). delly (rausch et al., ) was used for the analysis of chromosome structure variation (sv). all potential sv sites were detected and filtered for genomewide testing. by comparing the reads […]

2018
PMCID: 5818504
PMID: 29459759
DOI: 10.1038/s41598-018-21663-9

[…] than 0.05., copy-number variants (cnv) were predicted using control-freec ver 8.0, calculating variant changes by exon and using a breakpoint threshold of 1.5. translocations were assessed using delly, using standard parameters., msi status was infered from raw tumoral snv and microindels data using the msiseq package, using the author´s 526 tumoral exomes training database. msi […]

2017
PMCID: 5522335
PMID: 28489577
DOI: 10.18632/oncotarget.17253

[…] by the broad. germline snvs and indels were annotated with dbsnp 142, cosmic v54, annovar v2013-06-21 and funseq v0.1., somatic structural variants (svs) were called by applying crest valpha and delly v0.5.5 to the xenograft and matched normal genomes. the output of each tool was filtered to remove false positives and the resulting lists of variants were merged. somatic copy number variants […]

2017
PMCID: 5541750
PMID: 28768473
DOI: 10.1186/s12863-017-0541-3

[…] subsequently sequenced and analysed as previously described []. the genome data corresponding to roughly 15x coverage of the genome was made freely available under accession no. prjeb18113 []. the delly package [] was used to detect structural variants in the cleaned bam files. the snpeff software [], together with the umd3.1/bostau ensembl annotation [], was used to predict the functional […]

2017
PMCID: 5597596
PMID: 28904385
DOI: 10.1038/s41598-017-11523-3

[…] precluded their efficient filtering, we did not systematically investigate these polymorphisms (which are expected to represent only 1% of the total genomic variation). however, we used pindel, delly and igv to identify structural variants in the bd3 trio and in the gea, dr and nc mapping intervals (see below)., animals were specifically sampled according to their phenotype or origin, […]


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DELLY in publications

 (113)
PMCID: 5934390
PMID: 29725107
DOI: 10.1038/s41598-018-25260-8

[…] 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 […]

PMCID: 5931083
PMID: 29718005
DOI: 10.1038/sdata.2018.79

[…] 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 […]

PMCID: 5883058
PMID: 29615708
DOI: 10.1038/s41598-018-23802-8

[…] is an open-source, dynamic and fast tool to analyse the variation data produced from the resequencing experiments. super uses samtools v1.2 to call small variations (such as snps and dips) and delly tool v.0.6.5 for the svs (including deletions, inversions, duplications and translocations). snps and dips filtering was first performed using snpsift v3.6c. this tool set works on variant […]

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

[…] 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 […]

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

[…] 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 […]


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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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