VARIFI—Web-Based Automatic Variant Identification, Filtering and Annotation of Amplicon Sequencing Data
| Autor: | Peter Venhuizen, Arndt von Haeseler, Milica Krunic, Bettina Kaserer, Leonhard Müllauer |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
Computer science
Medicine (miscellaneous) lcsh:Medicine Single-nucleotide polymorphism Computational biology Article 03 medical and health sciences Annotation 0302 clinical medicine variant finding cancer Indel 030304 developmental biology 0303 health sciences amplicon sequencing business.industry lcsh:R pipeline Ion semiconductor sequencing personalized medicine Pipeline (software) Identification (information) 030220 oncology & carcinogenesis Personalized medicine business Personal genomics |
| Zdroj: | Journal of Personalized Medicine, Vol 9, Iss 1, p 10 (2019) Journal of Personalized Medicine Volume 9 Issue 1 |
| ISSN: | 2075-4426 |
| Popis: | Fast and affordable benchtop sequencers are becoming more important in improving personalized medical treatment. Still, distinguishing genetic variants between healthy and diseased individuals from sequencing errors remains a challenge. Here we present VARIFI, a pipeline for finding reliable genetic variants (single nucleotide polymorphisms (SNPs) and insertions and deletions (indels)). We optimized parameters in VARIFI by analyzing more than 170 amplicon-sequenced cancer samples produced on the Personal Genome Machine (PGM). In contrast to existing pipelines, VARIFI combines different analysis methods and, based on their concordance, assigns a confidence score to each identified variant. Furthermore, VARIFI applies variant filters for biases associated with the sequencing technologies (e.g., incorrectly identified homopolymer-associated indels with Ion Torrent). VARIFI automatically extracts variant information from publicly available databases and incorporates methods for variant effect prediction. VARIFI requires little computational experience and no in-house compute power since the analyses are conducted on our server. VARIFI is a web-based tool available at varifi.cibiv.univie.ac.at. |
| Databáze: | OpenAIRE |
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