Using regex for type validation

[Gribouillis]

You would get a better structured code with a function to handle each line

def is_vcf_line(line):
    columns = line.split('\t')
    return bool(
        re.match(r"^chr(?:[1-9][0-9]?|[XYM])$", columns[0]) 
        and re.match(r"^[1-9][0-9]*$", columns[1])
        and re.match(r"^[ATGC]$", columns[3]) 
        and re.match(r"^[ATGC]$", columns[4]))

def is_vcf(filename):
    with open(filename) as lines:
        return all(is_vcf_line(line) for line in lines)