Closed bartcharbon closed 3 years ago
Hi @bartcharbon , thanks for considering genmod!
Ok I will have a look at this.
@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.
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
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.
Yes that is correct, it should not be allowed in the INFO field. Good find! Open issue at VEP then :)
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.
When I try to run Genmod models with --vep, it throws an error and aborts:
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)