This is not an idiomatic Python code. You can easily make your Python code 
faster using list comprehensions. Python loops outside the comprehensions are 
slow. You should prefer using comprehesions and map/filter functions always 
when it's possible.

import sys import gzip

def main(vcf):
    vcf = gzip.open(vcf, 'r') toks = [ line.strip().split('t') for line in vcf 
if not line.startswith('#')]
    sample_toks = [ sample.split(':') for sample in toks[9:] ]
if __name__ == "__main__":
    main(sys.argv[1])

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