SNPfiltR: an R package for interactive and reproducible SNP filtering

• DOI: 10.22541/au.163976415.53888836/v1
• Publication Date: 2021-12-17T18:02:52Z
• Authors: Devon DeRaad
• Keywords: Benchmarking; R package; Representation

Here I describe the novel R package SNPfiltR and demonstrate its functionalities as backbone of a customizable, reproducible SNP filtering pipeline implemented exclusively via widely adopted programming language. extends existing by automating visualization key parameters such depth, quality, missing data, then allowing users to set filters based on optimized thresholds, all within single, cohesive working environment. All functions require vcfR object input, which can be easily generated reading dataset stored standard vcf file into an environment using function read.vcfR() from vcfR. Performance benchmarking reveals that for moderately sized datasets (up 50M genotypes with associated quality information), performs comparable efficiency current state art command-line-based programs. These results indicate most reduced-representation genomic datasets, is ideal choice investigating, visualizing, SNPs part documentable bioinformatic pipeline. The downloaded CRAN command [install.packages(“SNPfiltR”)], development version available GitHub at: (github.com/DevonDeRaad/SNPfiltR). Additionally, thorough documentation SNPfiltR, including multiple comprehensive vignettes, at website: (devonderaad.github.io/SNPfiltR/).