🧬 BEAGLE to VCF Converter (bgl2vcf.py)

This Python script converts phased BEAGLE v3.1 genotype files (.bgl) to the standardized VCF (Variant Call Format), using variant annotations from a corresponding PLINK .bim file.

⚠️ Heterozygous genotypes preserve allele order (e.g., 0|1 vs. 1|0), which is important for phased datasets. 📂 Input Files

BEAGLE v3.1 file (.bgl): Phased genotype data in BEAGLE format. PLINK .bim file (.bim): Contains SNP metadata (Chromosome, RSID, Position, Alleles) 🧾 Output

A .vcf file compatible with downstream tools and pipelines. Phased genotypes represented using VCF-style genotype encoding (0|0, 0|1, etc.). Any SNPs not found in the .bim file or with inconsistent allele encoding will be skipped or marked as missing (./.).

Usage

python bgl2vcf.py <input.bgl> <input.bim> <output.vcf>

Example

python bgl2vcf.py example.bgl example.bim output.vcf

🔧 Requirements

Python 3.x No external dependencies (uses only built-in libraries: sys, re)