VCF to Nexus or FASTA

Convert VCF files into nexus or fasta formats for use with the BEAST phylonco package https://github.com/bioDS/beast-phylonco

Requirements:

Python 3 with the pysam package. This can be installed with python3 -m pip install pysam.

Example VCF files

Example VCF files can be downloaded from https://github.com/amkozlov/cellphy-paper/blob/main/data/

The examples below use the VCF file E15.CellPhy.vcf from E15.zip

Citation for dataset: https://doi.org/10.1186/s13059-021-02583-w

Converting VCF to nexus

Full diploid genotype

Replace <vcf file> with the path of your VCF, and <nexus file> with the path of your Nexus file.

python3 src/vcf2nexus.py <vcf file> <nexus file> --encoding nd16

Example usage:

python3 src/vcf2nexus.py E15.CellPhy.vcf E15.CellPhy.nex --encoding nd16

Binary genotype

python3 src/vcf2nexus.py <vcf file> <nexus file> --encoding binary

Example usage:

python3 src/vcf2nexus.py E15.CellPhy.vcf E15.CellPhy.binary.nex --encoding binary

Converting VCF to fasta

Full diploid genotype

Replace <vcf file> with the path of your VCF, and <fasta file> with the path of your Fasta file.

python3 src/vcf2fasta.py <vcf file> <fasta file> --encoding nd16

Example usage:

python3 src/vcf2fasta.py E15.CellPhy.vcf E15.CellPhy.fasta --encoding nd16

Binary genotype

python3 src/vcf2fasta.py <vcf file> <fasta file> --encoding binary

Example usage:

python3 src/vcf2fasta.py E15.CellPhy.vcf E15.CellPhy.binary.fasta --encoding binary