I have imputed genotype data from the Haplotyle Reference Consortium in VCF format, and would like to convert to BGEN 1.3 (or 1.2).  I know that `qctool` version 2 support this, as does `plink` version 2.0.

I would like to inquire as to experiences anyone has had converting genotype probabilities (GP field in VCF) using these tools:

1. Is one tool preferred over the other?
2. Any caveats we should be aware of?

I would tend to use `plink`, as it is quite popular and actively developed, although the developers of `qctool` also developed the BGEN format, which may make it more ideal. I would assume these tools are equivalent for the task of converting VCF to BGEN, but your experience with this may suggest otherwise.
plink2 supports allelic dosages, not genotype probabilities.  So if your VCF GP field says P(0/0)=0.2, P(0/1)=0.52, P(1/1)=0.28, plink2 will just save "dosage(1)=1.08", and then when it's asked to export to BGEN it'll encode the dosage as P(0/0)=0, P(0/1)=0.92, P(1/1)=0.08.

When this is fine, plink2 is a good choice.  When this isn't good enough, use something like qctool.