vcf_parsing.py

from nucleus.io import vcf
from nucleus.util import variant_utils

with vcf.VcfReader('/home/ec2-user/DEEPVARIANT/NA12878_calls.vcf.gz') as reader:
  print('Sample names in VCF: ', ' '.join(reader.header.sample_names))
  for variant in reader:
      print(variant_utils.variant_type(variant)) # variant type
      print(variant.reference_name) # reference