Export_vcf with VEP

Hi, so I managed to run vep on my original vcf.bgz file, save a mt_vep for analysis but I’d like to save a vep.vcf.bgz file as well. So I tried this first:

mt_vep = hl.read_matrix_table('gs://...vep.mt')


hl.export_vcf(mt_vep, 'gs://...vep.vcf.bgz', parallel='header_per_shard', metadata=meta_orig)

Then I saw this warning:

2020-05-12 19:45:06 Hail: WARN: export_vcf: ignored the following fields:
    'vep' (row)

I obviously missed something in https://hail.is/docs/0.2/methods/impex.html#hail.methods.export_vcf, but what exactly please?

Thanks, Alan

So I think the relevant bit from the docs is:

Hail exports the fields of struct info as INFO fields, the elements of set<str> filters as FILTERS, the value of str rsid as ID, and the value of float64 qual as QUAL. No other row fields are exported.

I’m more on the engineering side than genetics side, so I don’t really use VEP, but I think the answer here is that anything you want to export from VEP has to go into a row annotation called info.

Thanks @johnc1231. I found this as well: https://discuss.hail.is/t/vcf-ignoring-vep-and-non-reference-samples-while-exporting

I can live with that. My main target is to get the data in a way I can query, like in Amazon Athena.