Primers trimming

[chadisaad]

Do V-pipe trim primers ? I can't find the information. (I see only this param in the conf file: primers_file=)

If yes, is it done post-alignment ?

[DrYak]

Hi!

Currently, we don't trim primers yet.
(the primers are only used for display on the visualisation, for now).

It is a feature planned in the future.
It will be done after the alignment and before the variant calling step.

In the immediate future, we have already plans to make our wariant caller ShoRAH - amplicon aware,
so SNV should not be affected by primers once that is moved to production.