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mdshw5/vcd_to_geno.py

Created October 13, 2018 20:47
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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)
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