I am exporting my matrix table to gcp storage, but it is ignoring fields vep(row) and non_reference_samples(row). How to overcome this and export all data and why is it happening.
VCF does not have a way to represent arbitrary structured data.
It is possible to put some information in the info field:
mt = mt.annotate_rows(info = mt.info.annotate(non_ref_samples=mt.non_reference_sample)))
this will not work for VEP though.