In 25Q3, mutation annotation vep --distance

Q&A
1

Dear DepMap team,
In DepMap 25Q3 mutation calling and annotation pipeline, which value(s) is/are used for the
vep --distance? It sets the minimum distance (in base pairs) for which upstream / downstream consequences will be assigned by the VEP. Do you use “–distance 0” or the default 5000?

Setting the --distance to 0 focus on the direct impacts, annotating those variants that are predicted to have a direct functional consequence on a feature, rather than those simply located nearby, and helps in reducing the amount of output if the default depth of annotation is not required.

Best regards,
Alice

2

Hi Alice,

Thank you for the suggestion! At the moment we are using the default distance. Previously, we did see certain variants being associated with a distant gene instead of the one it’s located in. To combat this, we customized the “–pick_order” parameter and that seemed to have helped significantly.

Are you seeing any variants currently in depmap that were assigned less direct consequences? We’d love to look into this further.

Thanks again,

Simone