Generate table of VEP gene hits and GO terms for each cultivar

[kshefchek]

For each VEP gene hit, collect the associated GO terms and generate a table with the fields cultivar, snp, gene, go terms, and any other interesting annotations from VEP.

Could use the GO VEP plugin (https://github.com/Ensembl/VEP_plugins/blob/release/101/GO.pm) or Planteome

[dlebauer]

@kshefchek what is the status of this?

[kshefchek]

I haven't made any progress other than https://github.com/genophenoenvo/terraref-datasets/pull/121/files @TomConlin is this something you could pick up?

[TomConlin]

Have not, but could look into it after next week (mid Feb?)

[TomConlin]

The snp/gene/cultivar parts already exist and I think gene-GO is addressed with
https://github.com/genophenoenvo/genomic_data/tree/master/GenomicApproachPrediction

please reopen there if there are additional feature desired (e.g. the extras field Ryan mentioned).

[TomConlin]

via: Slack

David LeBauer 7:19 AM
Is Tom on Slack? It’s not clear to me what is the next step with gene annotations data he prepared and I don’t want that to get dropped

Kent Shefchek 2 hours ago
I may have added some confusion with the wording in this ticket, looks like Tom and I have both added GO terms to the VEP output, but if iirc you want these added to the vcf file?