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VaRank: a simple and powerful tool for ranking genetic variants.

Authors
  • Geoffroy, Véronique1
  • Pizot, Cécile2
  • Redin, Claire2
  • Piton, Amélie3
  • Vasli, Nasim2
  • Stoetzel, Corinne4
  • Blavier, André5
  • Laporte, Jocelyn2
  • Muller, Jean6
  • 1 Laboratoire de Génétique médicale, UMR_S INSERM U1112, IGMA, Faculté de Médecine FMTS, Université de Strasbourg , Strasbourg , France ; IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg , Illkirch Cedex , France. , (France)
  • 2 IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg , Illkirch Cedex , France. , (France)
  • 3 IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg , Illkirch Cedex , France ; Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg , Strasbourg Cedex , France. , (France)
  • 4 Laboratoire de Génétique médicale, UMR_S INSERM U1112, IGMA, Faculté de Médecine FMTS, Université de Strasbourg , Strasbourg , France. , (France)
  • 5 Interactive Biosoftware , Rouen , France. , (France)
  • 6 IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg , Illkirch Cedex , France ; Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg , Strasbourg Cedex , France ; Laboratoire ICUBE, UMR CNRS 7357, LBGI, Université de Strasbourg , Strasbourg , France. , (France)
Type
Published Article
Journal
PeerJ
Publisher
PeerJ
Publication Date
Jan 01, 2015
Volume
3
Identifiers
DOI: 10.7717/peerj.796
PMID: 25780760
Source
Medline
Keywords
License
Unknown

Abstract

Background. Most genetic disorders are caused by single nucleotide variations (SNVs) or small insertion/deletions (indels). High throughput sequencing has broadened the catalogue of human variation, including common polymorphisms, rare variations or disease causing mutations. However, identifying one variation among hundreds or thousands of others is still a complex task for biologists, geneticists and clinicians. Results. We have developed VaRank, a command-line tool for the ranking of genetic variants detected by high-throughput sequencing. VaRank scores and prioritizes variants annotated either by Alamut Batch or SnpEff. A barcode allows users to quickly view the presence/absence of variants (with homozygote/heterozygote status) in analyzed samples. VaRank supports the commonly used VCF input format for variants analysis thus allowing it to be easily integrated into NGS bioinformatics analysis pipelines. VaRank has been successfully applied to disease-gene identification as well as to molecular diagnostics setup for several hundred patients. Conclusions. VaRank is implemented in Tcl/Tk, a scripting language which is platform-independent but has been tested only on Unix environment. The source code is available under the GNU GPL, and together with sample data and detailed documentation can be downloaded from http://www.lbgi.fr/VaRank/.

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