SVDetect protocols

SVDetect specifications

Information


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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  • person_outline SVDetect Team <>

Publication for SVDetect

SVDetect IN pipelines

 (3)
2017
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 [28]. 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 [29] aligning on different chromosomes, with unexpected strand […]

2016
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 [28] 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 […]

2015
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 [10] to predict structural variants (sv). the mps results were visualized on the integrative genomics viewer [11]. to identify sample-specific structural variants, the predicted svs […]

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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