msa2vcf

Turn a fasta-format MSA into one vcf per sequence.

msa2vcf msa.fasta ref_name

Install

pip install git+https://github.com/connor-lab/msa2vcf.git

Notes

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.