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• W2912902236 abstract "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." @default.
• W2912902236 created "2019-02-21" @default.
• W2912902236 creator A5002216760 @default.
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• W2912902236 date "2019-02-01" @default.
• W2912902236 modified "2023-09-25" @default.
• W2912902236 title "VARIFI—Web-Based Automatic Variant Identification, Filtering and Annotation of Amplicon Sequencing Data" @default.
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• W2912902236 doi "https://doi.org/10.3390/jpm9010010" @default.
• W2912902236 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/6463100" @default.
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• W2912902236 hasPublicationYear "2019" @default.
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