Export to BGEN

[hyanwong]

A number of large datasets are nowadays saved in BGEN format. Should we provide the ability to export variant data from tree sequences in BGEN format? Otherwise I assume we would have to go via vcf using e.g. qctool, and I don;t know if this loses any information:

with open("tmp.vcf", "wt") as f:
    ts.write_vcf(f)
subprocess.run(["./qctool", "-g", "tmp.vcf", "-og", "tmp.bgen"])

It could be that Gavin Band could help write a BGEN exporter? Has anyone asked him?

[jeromekelleher]

It's not trivial. What datasets are you thinking about?