SVDetect protocols

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chevron_left Deletion detection Insertion detection Structural variant detection Duplication detection Inversion detection CNV detection chevron_right
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SVDetect specifications


Unique identifier OMICS_00324
Name SVDetect
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.8b
Stability Stable
Maintained Yes



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Publication for SVDetect

SVDetect in pipelines

PMCID: 5225008
PMID: 28072833
DOI: 10.1371/journal.pone.0169935

[…] reads to the human reference genome grch37/hg19 using burrows-wheeler aligner (bwa)-mem with default parameters []. reads not aligning uniquely as well as pcr duplicates were not analysed further. svdetect was then used to identify potential translocations, inversions and large deletions/insertions from discordant paired-end data [] aligning on different chromosomes, with unexpected strand […]

PMCID: 4851415
PMID: 27128314
DOI: 10.1371/journal.pone.0154602

[…] read counts were calculated for carriers and controls and for each bin the ratio of meancarriers/meancontrols was calculated and logarithmized with base 2. structural variants were inferred by using svdetect [] and for short indels, the data were filtered for partially mapping reads (soft clips) and the mapping positions were analyzed for frequency and compared between the groups., real-time […]

PMCID: 4404611
PMID: 25901181
DOI: 10.1186/s13039-015-0129-4

[…] and sequenced 2x36 bases on a genome analyzer iix (illumina). a total of 31,960,052 out of 46,169,874 read-pairs could be aligned to the human genome assembly hg19 (grch37), using bwa []. using svdetect to search for structural variations [], we identified four read-pairs defining the breakpoints on the r(14) chromosome and the del(14) chromosome, with a resolution of appr. 1 kb […]

PMCID: 4504069
PMID: 26177635
DOI: 10.1186/s12920-015-0118-9

[…] breakpoints. also, short (75 – 100 bp) read mapping to the reference genome may generate false clusters of paired-end reads resulting in false sv calls. in order to confirm sv calls generated by svdetect and to establish breakpoints at the base-pair resolution, we performed a targeted de novo assembly for each sv call. de novo assembly is performed by progressively merging redundant dna […]

PMCID: 4696321
PMID: 26719771
DOI: 10.1186/s13039-015-0205-9

[…] aligning to different chromosomes, with unexpected strand orientation or increase/decrease in insert size, were extracted for further analysis. these “discordant” paired-reads were analysed by svdetect [] to predict structural variants (sv). the mps results were visualized on the integrative genomics viewer []. to identify sample-specific structural variants, the predicted svs […]

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SVDetect in publications

PMCID: 5823580
PMID: 29492199
DOI: 10.18632/oncotarget.23614

[…] a total of 167 million reads which, after mapping with stampy [] (version 1.0.13), resulted in a genome wide coverage of 8.65 fold with a local coverage of the transgene of 18.34 fold . subsequently svdetect [] (version 0.7) was used in interchromosomal rearrangement mode to identify the integration site of the alk transgene vector., to evaluate the overlap of the genes mutated in murine […]

PMCID: 5823676
PMID: 29168350
DOI: 10.1002/mgg3.346

[…] (bwa) (li & durbin, ). to annotate the unique svs, reads not aligning uniquely, were removed and the ones with unexpected orientation or aligning to different chromosomes were extracted using svdetect ( et al., ) and delly ( the predicted svs were compared with multiple in‐house mate pair datasets to identify […]

PMCID: 5679599
PMID: 29121641
DOI: 10.1371/journal.pone.0187617

[…] above 10 were kept for further analysis. we used three different software to identify structural variants (sv) from this mate-pair sequencing data: delly (doi: 10.1093/bioinformatics/bts378), svdetect [] and gasvpro []. all three software were used with default parameters. only translocations that were supported by more than 10 mate-pairs were considered as reliable candidate […]

PMCID: 4851415
PMID: 27128314
DOI: 10.1371/journal.pone.0154602

[…] ensure the detection of any potential variant., no significant large insertion/deletion was detected by copy number analysis in 5kbp bins. in addition no unambiguous variants were detected by using svdetect. therefore, to infer for smaller structural variants, we conducted an additional search for positions, were full length (150bp) reads of high sequence quality showed only a partial mapping, […]

PMCID: 4845489
PMID: 27118394
DOI: 10.1186/s12870-016-0788-2

[…] work and a substantial number of errors resulted from the de novo assembly of the dxwr genome using the ngs short reads. the essential work in this comparative strategy was using the software svdetect and the pipeline svfilter to detect structure variations (svs), which are being increasingly appreciated for their roles as a cause for phenotypic variations [–]. using the detected […]

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SVDetect institution(s)
Institut Curie, Paris, France; INSERM, U900, Paris, France; Mines ParisTech, Fontainebleau, France; INSERM, U380, Paris, France; CNRS, UMR3244, Université Pierre et Marie Curie, Paris, France
SVDetect funding source(s)
Supported by ‘Projet Incitatif Collaboratif Bioinformatique et Biostatistiques’ of the Institut Curie; Ligue Nationale Contre le Cancer; Institut National du Cancer.

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