Merging Imputed VCF with Reference Panel VCF

Question

[selplat21]

Hello,

I used a reference panel of 150 individuals to impute genotypes in 300 lower coverage samples using GLIMPSE.

I am wondering how people typically will merge the imputed data back with the reference panel so all samples can be analyzed together.

The problem is that the reference VCF will look like this: GT:GL:PL:GP 1/1:-89.7,-7.2,0:897,72,0:0,1.6809e-07,1

While the imputed VCF will look like this: GT:DS:GP:HS 0/1:0.994:0.006,0.994,0:682598