it depends of the VCF INFO and FORMAT available in your input.

If anyone will be interested I worked this out on ped plink files. First I recode A,C,T,G coding to 0,1,2 with --recode12,

then parse the ped file with this python script:

import random
import itertools

infile = open("subset.ped","r")
outfile = open("new_genotypes.ped","w")

check_11 = ('1','1')
check_22 = ('2','2')
def random_gen():
    choice_m = [check_11,check_22]
    res = random.choice(choice_m)
    return res

def parse_ped(ped_infile):
    check_12 = ('1','2')
    check_21 = ('2','1')

for line in ped_infile:
    row = line.split()
    head = row[0:6]
    genotype_old = row[6:]
    genotype_f = row[6:]
    it = iter(genotype_f)
    genotype_t = zip(it, it)
    for n,i in enumerate(genotype_t):
        if i == check_12 or i == check_21:
            genotype_t[n]=random_gen()
    print genotype_t[0:10]
    genotype_t = list(itertools.chain(*genotype_t))
    print genotype_t[0:10]

    new_line = head+genotype_t
    outfile.write(" ".join(new_line)+"\n")
outfile.close()

parse_ped(infile)