VCF File Analysis Tutorial

Introduction

This tutorial provides a step-by-step guide to analyzing VCF (Variant Call Format) files using a Bash script. The script performs basic analysis tasks such as counting variants, identifying SNPs and INDELs, and calculating the transition/transversion (Ts/Tv) ratio. It also generates summary statistics for further analysis.

Prerequisites

Before running the script, ensure you have the following tools installed:

• Bash: Pre-installed on most Unix-based systems.
• bcftools: Install using sudo apt-get install bcftools.
• vcftools: Install using sudo apt-get install vcftools.

Download the Script

Download the Bash script for VCF analysis:

Download vcf_analysis.sh

Script Overview

The script performs the following tasks:

1. Counts the total number of variants in the VCF file.
2. Identifies and counts SNPs and INDELs.
3. Calculates the Ts/Tv ratio.
4. Generates an allele frequency spectrum.
5. Saves the results in an output directory.

Running the Script

To run the script, follow these steps:

1. Download the script and place it in your working directory.
2. Make the script executable:

chmod +x vcf_analysis.sh

3. Run the script with your VCF file as input:

./vcf_analysis.sh your_file.vcf

4. The results will be saved in the vcf_analysis_output directory.

Output Files

The script generates the following output files:

• summary.txt: Contains summary statistics (total variants, SNPs, INDELs, Ts/Tv ratio).
• allele_freq.frq: Contains allele frequency data.
• TsTv.log: Log file for Ts/Tv ratio calculation.

Example

Here is an example of running the script:

./vcf_analysis.sh Ghir_A13G023930.vd.gene.SNPs.Gbio.1913.3kbud.HAU.recode.vcf

Output:

Analysis complete. Results are in the vcf_analysis_output directory.

Conclusion

This tutorial provides a simple yet powerful pipeline for analyzing VCF files. You can extend the script to include more advanced analyses as needed. Feel free to contribute to the project on GitHub.