SNPfiltR (Q69129)
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Interactively Filter SNP Datasets
| Language | Label | Description | Also known as |
|---|---|---|---|
| default for all languages | No label defined |
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| English | SNPfiltR |
Interactively Filter SNP Datasets |
Statements
4 September 2025
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Is designed to interactively and reproducibly visualize and filter SNP(single-nucleotide polymorphism) datasets. This R-based implementation of SNPand genotype filters facilitates an interactive and iterative SNP filtering pipeline, which can be documentedreproducibly via 'rmarkdown'. 'SNPfiltR' contains functions for visualizing various quality and missing data metrics for a SNP dataset, and then filteringthe dataset based on user specified cutoffs.All functions take 'vcfR' objects as input, which can easily begenerated by reading standard vcf (variant call format) files into R using the R package 'vcfR' authored by Knaus and Grünwald (2017) <doi:10.1111/1755-0998.12549>. Each 'SNPfiltR' function can return a newly filtered 'vcfR' object, which can then bewritten to a local directory in standard vcf format using the 'vcfR' package,for downstream population genetic and phylogenetic analyses.
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