Force heterozygous call to be homozygous at genotype format field

Question

[edavid.sant]

hello everybody

i have a multisample vcf with genotypes like:

GT:AD:DP ==> 1/2:0,37,2:39

The reads supporting the first alternate allele represents the 94.8% (37/39), so i want that when i put this variant into a fasta file, only the first alternate allele get inserted. For this, i want that all variants that are supported for more than 75% of reads get inserted in a new fasta reference file.

So, i figure out to transform that genotype to:

GT:AD:DP ==> 1/1:0,37,2:39

is that posible?

PD: i found bcftools setGT plugin does not allow me to set 1/1 or 2/2 genotypes, just missing or references genotypes.

Thank you for your help