Interactively Filter SNP Datasets
Vizualise how missing data thresholds affect sample clustering
Vizualise how missing data thresholds affect sample clustering
Filter a vcf file based on distance between SNPs on a given scaffold
Filter out heterozygous genotypes failing an allele balance check
Remove SNPs with more than two alleles
Hard filter a vcf file by depth and genotype quality (gq)
Vizualise and filter based on mean depth across all called SNPs
Vizualise, filter based on Minor Allele Count (MAC)
Vizualise missing data per sample, remove samples above a missing data...
Vizualise missing data per SNP, remove SNPs above a missing data cutof...
SNPfiltR: A package for interactively visualizing and filtering SNP da...
Is designed to interactively and reproducibly visualize and filter SNP (single-nucleotide polymorphism) datasets. This R-based implementation of SNP and genotype filters facilitates an interactive and iterative SNP filtering pipeline, which can be documented reproducibly via Rmarkdown. 'SNPfiltR' contains functions for visualizing various quality and missing data metrics for a SNP dataset, and then filtering the dataset based on user specified cutoffs. All functions take 'vcfR' objects as input, which can easily be generated by reading standard vcf (variant call format) files into R using the R package 'vcfR' (Knaus and Grünwald) (<doi:10.1111/1755-0998.12549>). Each 'SNPfiltR' function can return a newly filtered vcfR object, which can then be written to a local directory in standard vcf format using the 'vcfR' package, for downstream population genetic and phylogenetic analyses.