Introduction

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/.

Publications

  1. VaRank: a simple and powerful tool for ranking genetic variants.
    Cite this
    Geoffroy V, Pizot C, Redin C, Piton A, Vasli N, Stoetzel C, Blavier A, Laporte J, Muller J, 2015-01-01 - PeerJ

Credits

  1. Véronique Geoffroy
    Developer

    Laboratoire de Génétique médicale, UMR_S INSERM U1112, France

  2. Cécile Pizot
    Developer

    IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, France

  3. Claire Redin
    Developer

    IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, France

  4. Amélie Piton
    Developer

    IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, France

  5. Nasim Vasli
    Developer

    IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, France

  6. Corinne Stoetzel
    Developer

    Laboratoire de Génétique médicale, UMR_S INSERM U1112, France

  7. André Blavier
    Developer

    Interactive Biosoftware, Rouen, France

  8. Jocelyn Laporte
    Developer

    IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, France

  9. Jean Muller
    Investigator

    IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, France

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Summary
AccessionBT000165
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionFrance
Submitted ByJean Muller