VCF to CSV Conversion and LOH Plotting

This repository contains scripts for converting Variant Calling Format (VCF) file to CSV format and visualizing Loss of Heterozygosity (LOH) through plots.

Overview

1. Convert VCF to CSV Format: A script that processes VCF data and converts it into a structured CSV file. This allows easy analysis and visualization of VCF data. It counts RAF from VAF. And shows mirror image of the VAF and RAF.

2. LOH Plotting: A script to generate visualizations of Loss of Heterozygosity (LOH) based on VAF data, providing insights into genetic variations.

Prerequisites

awk
bcfools
R

Usage

./vcf_to_csv.sh -w <working_directory>