vcf_to_23-me

Convert VCF files into 23andMe-style genotype files using the OpenVar pipeline.

This project allows you to process VCF files through filtering, rsID checking, and conversion into a 23andMe-compatible format for personal research and genealogical use.

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Features

• Filter VCF variants based on sample-level FT values and chromosome.
• Remove variants that do not pass quality filters.
• Add missing rsIDs using a dbSNP VCF or remove variants without rsIDs.
• Convert the final VCF into a 23andMe-style genotype file (biallelic variants only).
• Excludes indels, ensuring only SNPs are included in the 23andMe-style output.

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Installation

1. Create the environment from environment.yml:

conda env create -f environment.yml
conda activate vcfto23me

2. install the pipeline:

pip install .

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Usage

Direct script execution

You can run the program directly with Python e.g.:

python vcf_to_23andme/main.py <input_dir> <output_dir> <genome_build> <sample.vcf>

Alternatively, run as a module using python -m:

python -m vcf_to_23andme.main <input_dir> <output_dir> <genome_build> <sample.vcf>

Arguments:

• <input_dir>: Directory containing the original VCF file.
• <output_dir>: Directory where output files will be written.
• <genome_build>: Either GRCh37 or GRCh38.
• <sample.vcf>: Name of the input VCF file.

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Output

The pipeline produces:

• Filtered VCF files at each processing stage.
• Final rsID-checked VCF.
• 23andMe-style genotype file: .23andme.txt.

23andMe-style file format

• Columns: rsid, chromosome, position, allele1, allele2.
• Only biallelic SNPs with valid rsIDs are included.
• Missing genotypes are represented as N.
• Includes a header indicating it was generated by OpenVar/vcf_to_23-me and is for personal research only.

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License

This program is licensed under the GNU Affero General Public License v3. See LICENSE.txt for details.