A1 Refereed original research article in a scientific journal
ShAn: An easy-to-use tool for interactive and integrated variant annotation
Authors: Rathinakannan VS, Schukov HP, Heron S, Schleutker J, Sipeky C
Publisher: PUBLIC LIBRARY SCIENCE
Publication year: 2020
Journal: PLoS ONE
Journal name in source: PLOS ONE
Journal acronym: PLOS ONE
Article number: ARTN e0235669
Volume: 15
Issue: 7
Number of pages: 7
ISSN: 1932-6203
DOI: https://doi.org/10.1371/journal.pone.0235669
Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/49258439
Abstract
Motivation Annotation of large amounts of generated sequencing data is a demanding task. Most of the currently available robust annotation tools, like ANNOVAR, are command-line based tools which require a certain degree of programming skills. User-friendly tools for variant annotation of sequencing data with graphical interface are under-represented.
Results We have developed an interactive application, which harnesses the easy usability of R Shiny and combines it with the versatile annotation features of ANNOVAR. This application is easy to use and gives comprehensive annotations for user supplied vcf files using multiples databases. The output table contains the list of variants and their corresponding annotation presented within the graphical interface. In addition, the annotation results are downloadable as text file.
Motivation Annotation of large amounts of generated sequencing data is a demanding task. Most of the currently available robust annotation tools, like ANNOVAR, are command-line based tools which require a certain degree of programming skills. User-friendly tools for variant annotation of sequencing data with graphical interface are under-represented.
Results We have developed an interactive application, which harnesses the easy usability of R Shiny and combines it with the versatile annotation features of ANNOVAR. This application is easy to use and gives comprehensive annotations for user supplied vcf files using multiples databases. The output table contains the list of variants and their corresponding annotation presented within the graphical interface. In addition, the annotation results are downloadable as text file.
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