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:
- Is one tool preferred over the other?
- 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.