SNP-Distance-Matrix-Generator

A script to calculate pairwise SNP distances from a core-genome VCF file and generate a distance matrix. Designed for bioinformatics workflows, this tool provides an easy-to-use interface for analyzing genomic similarities and differences.

Features

• Calculates pairwise SNP distances between samples in a VCF file.
• Outputs a distance matrix as a CSV file.
• Optionally simplifies the matrix by removing duplicate distances and diagonal entries using the -simplify flag.
• Automatically orders samples by their average SNP distances for better pattern visualization.

Requirements

• R (version 3.5 or higher)
• vcfR package (installed automatically if missing)

Usage

Run the script from the command line:

Rscript snps-matrix.R [path to core-vcf] [-simplify (optional)]

Examples

1. Generate Full Distance Matrix:

Rscript snps-matrix.R core.vcf

Output: distance_matrix_ordered.csv

2. Generate Simplified Distance Matrix:

Rscript snps-matrix.R core.vcf -simplify

Output: distance_matrix_simplified.csv

Output

• Rows/Columns: Sample IDs (from the VCF file).
• Values: SNP distances between pairs of samples.
• Simplified Matrix: Lower triangle and diagonal entries are replaced with empty cells.

Contact

For questions or issues, please contact sb474@st-andrews.ac.uk.