variant details not shown in epitope prediction result tsv when using VEP as annotation tool

nf-core / epitopeprediction

A bioinformatics best-practice analysis pipeline for epitope prediction and annotation

https://nf-co.re/epitopeprediction

MIT License

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variant details not shown in epitope prediction result tsv when using VEP as annotation tool #240

Open qbicStefanC opened 6 months ago

qbicStefanC commented 6 months ago

Description of the bug

Currently the columns variant details (genomic) and variant details (protein) are only filled when using snpeff as annotation tool , not VEP. Is there a chance to integrate VEP in a way that these columns are also filled when using VEP?

Command used and terminal output

No response

Relevant files

No response

System information

No response

christopher-mohr commented 6 months ago

Hi Stefan, thanks for reporting. If I remember correctly we had a short discussion on that before and we found out that thisis the case if variant details are not part of the VEP annotated variants. Do you have an update with respect to that?

qbicStefanC commented 6 months ago

Hi Chris, yes, true. I can look into this again from the sarek input.

Stefan