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elowy01/vcf_parsing.py

Last active August 2, 2023 19:32
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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
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