VaRank: a simple and powerful tool for ranking genetic variants
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 on...
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| Format: | Article |
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PeerJ Inc.
2015-03-01
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| Online Access: | https://peerj.com/articles/796.pdf |
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| author | Véronique Geoffroy Cécile Pizot Claire Redin Amélie Piton Nasim Vasli Corinne Stoetzel André Blavier Jocelyn Laporte Jean Muller |
| author_facet | Véronique Geoffroy Cécile Pizot Claire Redin Amélie Piton Nasim Vasli Corinne Stoetzel André Blavier Jocelyn Laporte Jean Muller |
| author_sort | Véronique Geoffroy |
| collection | DOAJ |
| description | 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/. |
| first_indexed | 2024-03-09T06:36:55Z |
| format | Article |
| id | doaj.art-19fad63a586c4b0cb66d1f2b1adc1c95 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:36:55Z |
| publishDate | 2015-03-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-19fad63a586c4b0cb66d1f2b1adc1c952023-12-03T10:56:19ZengPeerJ Inc.PeerJ2167-83592015-03-013e79610.7717/peerj.796796VaRank: a simple and powerful tool for ranking genetic variantsVéronique Geoffroy0Cécile Pizot1Claire Redin2Amélie Piton3Nasim Vasli4Corinne Stoetzel5André Blavier6Jocelyn Laporte7Jean Muller8Laboratoire de Génétique médicale, UMR_S INSERM U1112, IGMA, Faculté de Médecine FMTS, Université de Strasbourg, Strasbourg, FranceIGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch Cedex, FranceIGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch Cedex, FranceIGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch Cedex, FranceIGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch Cedex, FranceLaboratoire de Génétique médicale, UMR_S INSERM U1112, IGMA, Faculté de Médecine FMTS, Université de Strasbourg, Strasbourg, FranceInteractive Biosoftware, Rouen, FranceIGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch Cedex, FranceIGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch Cedex, FranceBackground. 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/.https://peerj.com/articles/796.pdfNext generation sequencingVariant rankingHuman geneticsMolecular diagnosticMutation detectionAnnotation |
| spellingShingle | Véronique Geoffroy Cécile Pizot Claire Redin Amélie Piton Nasim Vasli Corinne Stoetzel André Blavier Jocelyn Laporte Jean Muller VaRank: a simple and powerful tool for ranking genetic variants PeerJ Next generation sequencing Variant ranking Human genetics Molecular diagnostic Mutation detection Annotation |
| title | VaRank: a simple and powerful tool for ranking genetic variants |
| title_full | VaRank: a simple and powerful tool for ranking genetic variants |
| title_fullStr | VaRank: a simple and powerful tool for ranking genetic variants |
| title_full_unstemmed | VaRank: a simple and powerful tool for ranking genetic variants |
| title_short | VaRank: a simple and powerful tool for ranking genetic variants |
| title_sort | varank a simple and powerful tool for ranking genetic variants |
| topic | Next generation sequencing Variant ranking Human genetics Molecular diagnostic Mutation detection Annotation |
| url | https://peerj.com/articles/796.pdf |
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