ICCFGG 2022
#15 VariantscanR – an R package as a clinical tool for variant filtering of known phenotype-associated variants in domestic animals. (student)
Fréderique Boeykens1 , Sofie Bhatti1, Luc Peelman1, Bart J. G. Broeckx1 frederique.boeykens@ugent.be 1Ghent University, Ghent, Belgium Background:
Since the introduction of next-generation sequencing (NGS) techniques, whole-exome sequenc- ing (WES) and whole-genome sequencing (WGS) have not only revolutionized research, but also diagnostics. The gradual switch from single gene testing to WES and WGS required a different set of skills, given the amount and type of data generated, while the demand for standardization remained. However, most of the tools currently available are solely applicable for human analysis because they require access to specific databases and/or simply do not support other species. Clinical genetics in animals comes with the additional complexity that genetic diversity is often dangerously low due to the breeding history. Combined, there is a clear need for an easy-to-use, flexible tool that allows standardized data processing and preferably, monitoring of genetic diversity as well. For this reason, we developed the R-package variantscanR that allows easy and straight- forward identification and prioritization of known phenotype-associated variants identified in dogs and other domestic animals. Results: The R-package variantscanR enables the filtering of variant call format (VCF) files for the presence of known phenotype-associated variants and allows for the estimation of genetic diversity using multi-sample VCF files. Next to this, additional functions are available for the quality control and processing of user-defined input files to make the workflow as easy and straightforward as possible. This user-friendly approach enables the standardisation of complex data analysis in clinical settings.
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