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GASV specifications

Information


Unique identifier OMICS_01352
Name GASV
Alternative name Geometric Analysis of Structural Variants
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Publication for Geometric Analysis of Structural Variants

GASV in publications

 (8)
PMCID: 5167064
PMID: 27540267
DOI: 10.1093/bioinformatics/btw541

[…] accessible for researchers unfamiliar with command-line tools and enables immediate visual inspection of read pair configurations in genomic regions with predicted svs (see ). fig. 3. , we chose geometric analysis of structural variants (gasv) 2.0 (, http://compbio.cs.brown.edu/projects/gasv/) for integration. its development focused on the human genome, but it has also been tested […]

PMCID: 5026262
PMID: 27499133
DOI: 10.1093/molbev/msw161

[…] according to simulation results, the detection of deletions with respect to the p. trichocarpa reference genome was performed by combining the results of the two sv detection methods delly () and gasv ()., delly was run with default parameters and the results were filtered by selecting only the deletions having a length included in the range 1–25 kb and by discarding those supported by less […]

PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] the average insert size. several tools based on the detection of sv signatures from clusters of read-pairs have been reported in the literature including breakdancer, variationhunter, pemer, and gasv (chen et al., ; hormozdiari et al., , ; korbel et al., ; sindi et al., ). remarkably, pemer can be exploited for the identification of linked insertions (medvedev et al., )., clusters […]

PMCID: 4403555
PMID: 25941534
DOI: 10.3389/fgene.2015.00149

[…] genomic hybridization (cgh; ). a number of methods have also been developed to call svs from sequencing data, including re-sequencing and de novo assembly methods such as multibreak-sv (), gasv (), lumpy (), delly (), cn.mops (), as well as methods reviewed in , . epigenetic variations are the modifications on dna or chromatin without altering the dna sequence. before ngs, detection […]

PMCID: 4132716
PMID: 25034695
DOI: 10.1093/nar/gku590

[…] cell lines. the detections by delly and breakdancer were merged to obtain the final sv call set. for glc1 cell lines, a further analysis of candidate svs was made by using hydra (v. 0.5.3) () and gasv (v. 2.0) (). gasv was also employed in colo320 cell lines. hydra analysis was performed as recommended by its authors: we first realigned all discordant and unmapped reads using novoalign […]


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GASV institution(s)
Division of Applied Mathematics, Center for Computational Molecular Biology, Brown University, Providence, RI, USA

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