VCF to CSV Converter

This repository contains a bash script vcf_to_csv.sh which is designed to convert VCF (Variant Call Format) files into CSV (Comma-Separated Values) format with robust handling for encoded fields and proper encapsulation of output fields in quotes.

Overview

The vcf_to_csv.sh script simplifies the conversion of genomic data from VCF files into a more universally accessible CSV format. It encapsulates each value within quotes to ensure compatibility with CSV parsers and provides functionality to decode specific encoded fields like comments and effects.

Key Features:

Converts VCF files to CSV format.
Handles encoded fields by decoding them from Base64.
Encapsulates all output fields in quotes to ensure CSV format integrity.
Allows specifying delimiters for the output file (comma or tab).

Usage

To use the script, you must provide the input VCF file and specify the output file name and delimiter. The script usage is as follows:

./vcf_converter.sh -i <input_file> -o <output_file> -d <delimiter>

Parameters:

-i <input_file>: The path to the input VCF file.
-o <output_file>: The path to the output CSV file (default: output.csv).
-d <delimiter>: Delimiter for the CSV output (',' for CSV, '\t' for TSV; default: ',').
-h: Display help and exit.

Example:

./vcf_to_csv.sh -i sample.vcf -o sample.csv -d ","

Requirements

GNU Awk (Gawk): Used for processing the VCF files.
Bash: For scripting and control flow.

Installation

No specific installation steps are required if you have Bash and Gawk already installed on your system. You can simply clone this repository and run the script.

git clone https://github.com/your-username/vcf-to-csv-converter.git
cd vcf-to-csv-converter
chmod +x vcf_to_csv.sh
./vcf_to_csv.sh -i your_input.vcf -o your_output.csv

Configuration

The script includes adjustable settings for the fields that need to be decoded from Base64. Modify the ENCODED_FIELDS variable within the script to match the fields in your VCF that are encoded and need decoding:

ENCODED_FIELDS="JsiDbComment JsiDbEffect JsiDbSig"

Output

The script generates a CSV file where each line corresponds to a VCF entry, and fields are separated by the specified delimiter. The first line contains headers derived from the VCF file's metadata.

Troubleshooting

Ensure that the input VCF file is properly formatted and contains the standard VCF headers.
If output fields are not decoded properly, check the ENCODED_FIELDS setting and ensure that the field names match those in your VCF file.

Contributing

Contributions to improve the script or address bugs are welcome. Please submit a pull request or an issue through GitHub.

berntpopp/vcf-converter