VaRank: a simple and powerful tool for ranking genetic variants
Véronique Geoffroy1, Cécile Pizot2, Claire Redin2
1Laboratoire 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.
Peerj
|March 18, 2015
Summary
Identifying genetic variants from high-throughput sequencing is challenging. VaRank is a new tool that ranks genetic variants, aiding disease gene discovery and molecular diagnostics.
Area of Science:
- Genetics
- Bioinformatics
- Computational Biology
Background:
- Genetic disorders often stem from single nucleotide variations (SNVs) or small insertion/deletions (indels).
- High-throughput sequencing (HTS) has expanded the catalog of human genetic variations, including disease-causing mutations.
- Distinguishing significant variants among numerous others presents a considerable challenge for researchers and clinicians.
Purpose of the Study:
- To develop a computational tool for prioritizing and ranking genetic variants identified through HTS.
- To facilitate the integration of variant analysis into next-generation sequencing (NGS) bioinformatics pipelines.
- To assist in disease-gene identification and the setup of molecular diagnostics.
Main Methods:
- Developed VaRank, a command-line tool for variant ranking.
- VaRank scores and prioritizes variants annotated by Alamut Batch or SnpEff.
- Supports the Variant Call Format (VCF) for seamless integration into NGS workflows.
- Incorporates a barcode feature for rapid visualization of variant presence and zygosity status.
Main Results:
- VaRank effectively scores and ranks genetic variants.
- The tool enables quick assessment of variant presence and zygosity (homozygote/heterozygote status).
- Successfully applied in disease-gene identification and molecular diagnostics for numerous patients.
Conclusions:
- VaRank is a platform-independent tool implemented in Tcl/Tk, tested on Unix.
- The source code is available under GNU GPL with sample data and documentation.
- VaRank simplifies the complex task of variant prioritization in HTS data analysis.
Keywords:
AnnotationBarcodeHuman geneticsMolecular diagnosticMutation detectionNext generation sequencingSoftwareVariant rankingMore Related Videos
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