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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

Versioning


No version available

Documentation


Publication for Geometric Analysis of Structural Variants

GASV citations

 (6)
library_books

ReadXplorer 2—detailed read mapping analysis and visualization from one single source

2016
Bioinformatics
PMCID: 5167064
PMID: 27540267
DOI: 10.1093/bioinformatics/btw541

[…] ection 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 successful […]

library_books

Whole genome sequencing and analysis of Swarna, a widely cultivated indica rice variety with low glycemic index

2015
Sci Rep
PMCID: 4464077
PMID: 26068787
DOI: 10.1038/srep11303

[…] osome regions were defined as hyper-varying regions if SNPs/kb > 5 or InDels/kb > 1, and hypo-varying regions if SNPs/kb < 0.1 or InDels/kb < 0.01. Copy number variation (CNV) analysis was done using GASV software (https://code.google.com/p/gasv/). […]

library_books

A review of study designs and statistical methods for genomic epidemiology studies using next generation sequencing

2015
Front Genet
PMCID: 4403555
PMID: 25941534
DOI: 10.3389/fgene.2015.00149

[…] omparative 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 of […]

library_books

Computational tools for copy number variation (CNV) detection using next generation sequencing data: features and perspectives

2013
BMC Bioinformatics
PMCID: 3846878
PMID: 24564169
DOI: 10.1186/1471-2105-14-S11-S1

[…] reduce false positives in deletion identification, the tool requires that the deletion identified by the PEM approach should also be confirmed by the lower read depth in the same genomic regions.The GASV-Pro is another successful example of a combinatorial method. It was upgraded from a single PEM-based tool, GASV (Geometric Analysis of Structural Variants), and incorporated read depth informatio […]

library_books

Endogenous Retrovirus EAV HP Linked to Blue Egg Phenotype in Mapuche Fowl

2013
PLoS One
PMCID: 3747184
PMID: 23990950
DOI: 10.1371/journal.pone.0071393

[…] hicken.genomics.org.cn/chicken/) SNP databases, and the functional consequences of novel SNPs were summarized using Ensembl's Variant Effect Predictor (). Structural variants (SVs) were called using GASV 2.0 and filtered to produce a set of SVs unique to oocyan samples and within the mapping interval (Gga1:67,051,487–67,364,512). Reads spanning the SV boundaries were assembled into contigs and B […]

library_books

Consistency based detection of potential tumor specific deletions in matched normal/tumor genomes

2011
BMC Bioinformatics
PMCID: 3283309
PMID: 22152084
DOI: 10.1186/1471-2105-12-S9-S21

[…] sues of the same patient: A tumor and a normal sample. Paired-end reads were mapped to a reference genome and discordant mappings were assembled to maximal valid clusters calling for deletions (using GASV []). These deletions were then analyzed in terms of consistency: Can all mappings and deletions be explained by assuming that all read pairs were read from the mapped positions in a diploid set o […]

Citations

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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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