Genmod models '--vep' option throws exception

[bartcharbon]

When I try to run Genmod models with --vep, it throws an error and aborts:

genmod.commands.annotate_models: 'list' object has no attribute 'split'
Aborted!

If I use the same file with bcftools +split-vep to extract the gene field from VEP and use this field in de "keyword" option for Genmod it works fine. (But intron/exon info is lost this way)

[moonso]

Hi @bartcharbon , thanks for considering genmod!

Ok I will have a look at this.

[moonso]

@bartcharbon could you provide a small example from the file where this error occur? There are several test cases using VEP and we use it all the time so I am a bit curious about what is going on.

[bartcharbon]

Hi @moonso

Thanks for looking into this so quickly!

I attached a minimal example zip file (since github does not support vcf and ped attachments)

the command I use: genmod models ./example.vcf -f ./example.ped --vep -p 4

We are using version 3.7.3 of Genmod. For VEP we use version 100

example.zip

[bartcharbon]

I did some more digging myself, and I think I identified the problem: I think this HgvsP notation in the CSQ INFO field is causing the problem: NP_001116849.1:p.Gly78= If I remove the "=" sign the problem is solved.

I guess that an "=" as part of a INFO value is not allowed, so the issue might be in VEP instead of Genmod.

[moonso]

Yes that is correct, it should not be allowed in the INFO field. Good find! Open issue at VEP then :)

[bartcharbon]

I found an exisiting issue: https://github.com/Ensembl/ensembl-vep/issues/430

The problem is not in VEP but in the configuration we run it with, we run with "--no_escape" which leads to this behaviour.