Turn a fasta-format MSA into one vcf per sequence.
msa2vcf msa.fasta ref_name
pip install git+https://github.com/connor-lab/msa2vcf.git
VCF position is based on reference position.
IUPAC bases:
- Ref base is stripped from list of potentials
- Variant AF is given as 1/IUPAC redundancy
Pretty much all Python stdlib and all that entails - no input checking, no brakes.