Annotate variants with gene information

annotate_variants.py is a Python script that annotates a VCF file with gene information from a GenBank reference file. It matches variant positions to known genes and adds two extra columns: Gene_ID, indicating the corresponding gene or labeling it as Intergenic, and Variant_Effect, describing the variant’s functional context (e.g., Coding, Intergenic).

Features

• Extracts gene annotations from a GenBank reference file.
• Matches variant positions in a VCF file to genes.
• Adds a Gene_ID column to the annotated VCF.
• Supports command-line arguments for flexibility.
• Preserves the original VCF structure and headers.

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Installation

1. Install required dependencies

Make sure you have Python 3+ and biopython installed.

pip install biopython

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Usage

Run the script with the following arguments:

python annotate_variants.py -i variants.vcf --ref reference.gbk -o annotated.vcf

Argument	Description
-i, --input_vcf	Input VCF file with variant data
--ref, --reference_gbk	Reference GenBank file containing gene annotations
-o, --output_vcf	Output annotated VCF file

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Example

1. Download a reference GenBank file

You can download a GenBank file from NCBI using:

esearch -db nucleotide -query MH910496.1 | efetch -format Genbank > reference.gbk

2. Run the annotation script

python annotate_variants.py -i variants.vcf --ref reference.gbk -o annotated_variants.vcf

3. Output (annotated VCF file)

#CHROM  POS     ID      REF     ALT     Gene_ID     Variant_Effect
chr1    500     .       A       T       ABC1        Coding
chr1    1200    .       G       C       Intergenic  Intergenic
chr1    3000    .       T       A       XYZ2        Coding

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Troubleshooting

• Error: FileNotFoundError → Ensure the input files exist.
• Error: biopython not found → Install it using pip install biopython.
• Incorrect gene matches? → Check if the GenBank file contains complete gene annotations.

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License

This project is open-source and available under the MIT License.

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Contributions

Contributions are welcome! If you have suggestions, feel free to submit a pull request.

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