Is it possible to create a file of genotype dosages from a VCF using the phred-scale likelihoods (PL) given for each possible genotype? For example the genotype call:
1 497 . C T 1882.89 PASS GT:AD:DP:GQ:PL 0/0:3,0:3:0:0,0,45
where the PL for 0/0 is 0 and for 0/1 is also 0 would be assigned a dosage of 0.5 because there is an exact uncertainty between whether the genotype should be homozygous reference (which is given a value of 0) and heterozygous (which is given a value of 1).