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Protocols

VariantDB specifications

Information


Unique identifier OMICS_20259
Name VariantDB
Restrictions to use Academic or non-commercial use
Database management system MySQL
Community driven No
Data access Browse
User data submission Allowed
Maintained Yes

Maintainer


  • person_outline Geert Vandeweyer

Additional information


http://143.169.238.105/variantdb/index.php?page=tutorial&topic=intro http://143.169.238.105/variantdb/index.php?page=tutorial&topic=filters http://143.169.238.105/variantdb/index.php?page=tutorial

Publication for VariantDB

VariantDB citations

 (3)
call_split

Candidate Gene Resequencing in a Large Bicuspid Aortic Valve Associated Thoracic Aortic Aneurysm Cohort: SMAD6 as an Important Contributor

2017
Front Physiol
PMCID: 5469151
PMID: 28659821
DOI: 10.3389/fphys.2017.00400
call_split See protocol

[…] ed pipeline, followed by variant calling with the Genome Analysis Toolkit Unified Genotyper (DePristo et al., ). Variants were subsequently annotated and filtered with the in-house developed database VariantDB (Vandeweyer et al., ), which uses ANNOVAR. Heterozygous coding or splice site (±2 bp from exon-intron boundaries for nucleotide substitution, and ±5 bp for multi-bp deletions or insertions) […]

library_books

A Robust Protocol to Increase NimbleGen SeqCap EZ Multiplexing Capacity to 96 Samples

2015
PLoS One
PMCID: 4397063
PMID: 25875648
DOI: 10.1371/journal.pone.0123872

[…] ATK v.2.8.1 indel realignment and base quality recalibration [, ]. Variants were called with GATK Unified Genotyper after which annotation, filtering and interpretation of the variants was done using VariantDB []. […]

call_split

A SWI/SNF related autism syndrome caused by de novo mutations in ADNP

2014
Nat Genet
PMCID: 3990853
PMID: 24531329
DOI: 10.1038/ng.2899
call_split See protocol

[…] Penzberg, Germany), and sequencing on HiSeq 2000 (Illumina Inc, San Diego, CA, USA), all following standard protocols. Data analysis was performed using Galaxy (see URLs)-. Variants were filtered by VariantDB (see URLs, manuscript in preparation) to exclude variants with (1) low quality, using thresholds based on correlation between NGS data and SNP-chip genotyping; (2) intronic or intergenic loc […]

Citations

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VariantDB institution(s)
Department of Medical Genetics, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Center Antwerp, University and University Hospital of Antwerp, Antwerp, Belgium; Department of Medical Genetics, University Hospital of Antwerp, Antwerp, Belgium
VariantDB funding source(s)
Supported by the Belgian National Fund for Scientific Research-Flanders (FWO), IWT/TBM (grant 110700) and the Fondation Leducq.

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