Manage the three possible genotypes in vcf

[tdelhomme]

Instead of only consider variant (0/1) or not (0/0) in term of genotype, now manage the three possible genotypes:
0/0 for not being a variant
0/1 for being a heterozygous variant
1/1 for being a homozygous variant
For that, consider a variant (QVAL>threshold) as homozygous if and only if its allelic fraction exceeds 0.75.