SNPfiltR

SNPfiltR filters single nucleotide polymorphisms (SNPs) and provides interactive visualization and reproducible filtering workflows for VCF-derived SNP datasets within R.

Key Features:

• Interactive Visualization: Automates visualization of sequencing depth, quality scores, and missing data proportions to support threshold selection.
• Reproducibility: Implements all functionality exclusively in R, enabling scripted workflows and reproducible recording of filtering steps.
• Integration with VCF Data: Operates on vcfr objects produced by read.vcfR() from the vcfr package to directly process standard VCF files in R.
• Performance and Accuracy: Reported benchmarking indicates filtering accuracy and efficiency comparable to leading command-line programs for datasets up to 50 million genotypes.

Scientific Applications:

• Genomic Data Quality Assessment: Visualizes key quality metrics to inform and justify SNP filtering criteria.
• Customizable Filtering Pipelines: Enables tailoring of filtering criteria and functions to specific experimental designs and datasets.
• Reproducible Research Practices: Supports creation of reproducible SNP filtering workflows within the R environment for consistent analyses across studies.

Methodology:

SNP data are read from VCF files into R as vcfr objects using read.vcfR() from the vcfr package; a range of filtering functions and visualizations of sequencing depth, quality scores, and missing data proportions are used to assess and optimize dataset quality.