biostars 203117

example.py

from pyfaidx import FastaVariant
import vcf

samples = vcf.Reader(open('calls.vcf.gz', 'r')).samples

for sample in samples:
  with FastaVariant('reference.fasta', 'calls.vcf.gz', sample=sample, het=True, hom=True) as consensus:
    with open(sample + '.fasta', 'w') as sample_fasta:
      for record in consensus:
        sample_fasta.write('>' + record.long_name)
        sample_fasta.write(str(record))