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Protocols

SVA specifications

Information


Unique identifier OMICS_00190
Name SVA
Alternative names Sequence Variant Analyzer, SequenceVariantAnalyzer
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Stability Stable
Maintained No

Taxon


  • Primates
    • Homo sapiens

Versioning


No version available

Maintainer


This tool is not available anymore.

Publication for Sequence Variant Analyzer

SVA citations

 (13)
library_books

Rational confederation of genes and diseases: NGS interpretation via GeneCards, MalaCards and VarElect

2017
Biomed Eng Online
PMCID: 5568599
PMID: 28830434
DOI: 10.1186/s12938-017-0359-2

[…] uality score ≥50, ratio of (reads supporting variant)/(reads supporting reference): 0.2–5.0, and reads supporting indel ≥3. Annotation was performed using either SnpEff-3.3 (Ensembl 73 database), the SequenceVariantAnalyzer software (SVA), DNAnexus software (Palo Alto, CA, USA), and an in-house script using ANNOVAR80 and the GeneCards database annotation.Only protein-altering variants (stop gain/l […]

call_split

Dysregulation of WTI (−KTS) is Associated with the Kidney Specific Effects of the LMX1B R246Q Mutation

2017
Sci Rep
PMCID: 5216339
PMID: 28059119
DOI: 10.1038/srep39933
call_split See protocol

[…] sequencer. Reads were aligned to the Human Reference genome (HG 18) using the BWA software. Single nucleotide variants were called usingSAMtools. The variants were annotated to Ensembl 50_36 l using SequenceVariantAnalyzer (SVA) and were analyzed using the ATAV software. […]

library_books

Var2GO: a web based tool for gene variants selection

2016
BMC Bioinformatics
PMCID: 5123234
PMID: 28185576
DOI: 10.1186/s12859-016-1197-0

[…] focused on variant rather than gene annotation, and all exclusively usable from command line. One available tool for visualizing annotated sequence variants and interacting with the VCF input file is SVA [], which requires high-performance workstations or servers to properly work. Other available software include VCF-Miner [] and EVA [], but both of them need the installation of a complete web sta […]

library_books

Rare hereditary COL4A3/COL4A4 variants may be mistaken for familial focal segmental glomerulosclerosis

2014
PMCID: 4245465
PMID: 25229338
DOI: 10.1038/ki.2014.305

[…] Whole-exome sequencing was performed on 25 families. The Illumina TruSeq kit was used to create a 62Mb target region exome library and a customized sequence variant analyzer software was used. Podocyte-exome sequencing was performed on 38 families. An exon capture sequence chip containing 2,400 genes that are enriched in the podocyte was designed […]

library_books

Annotate it: a Swiss knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease

2012
Genome Med
PMCID: 3580443
PMID: 23013645
DOI: 10.1186/gm374

[…] on analyses or looking at different underlying genetic disease models (VAAST []). A variety of tools try to be more comprehensive and provide a streamlined approach by tackling both steps (KGGSeq [], SVA []).Although current tools have matured significantly, they still possess several limitations. First there is the 'red queen' annotation problem. As functional information is constantly evolving, […]

library_books

Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows

2012
Genes
PMCID: 3490498
PMID: 23139896
DOI: 10.3390/genes3030545

[…] plored and embedded in workflow at least three different frameworks to call SNPs and Indels from whole genome alignment data and produce a comprehensive mutation/functional analysis report ().For the Sequence Variant Analyzer (SVA, http://www.svaproject.org []) v1.0 workflow, after SNPs and Indels have been called with SAMTOOLS [] (http://samtools.sourceforge.net/) and CNVs have been called with “ […]

Citations

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SVA institution(s)
Center for Human Genome Variation, Duke University School of Medicine, Durham, NC, USA; Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
SVA funding source(s)
Supported by the Bill & Melinda Gates Foundation (grant 157412); National Institute of Allergy and Infectious Diseases Center for HIV/AIDS Vaccine Immunology (grant AI067854); National Institute of Neurological Disorders and Stroke (grant RC2NS070344); National Institute of Mental Health (grant RC2MH089915).

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