gencove to DNA.land

vcd_to_geno.py

import vcf

file = ''
with open('outfile.txt', 'w') as out:
  for variant in vcf.Reader(open(file)):
    if len(variant.FILTER) == 0:
      if variant.is_snp:
        for sample in variant.samples:
          ref, alt = sample.gt_bases.replace('|', '/').split('/')
          print(variant.CHROM, str(variant.POS), ref, alt, sep='\t', file=out)