Generalise the ExACpLI.pm

[henrikstranneheim]

I would like to use the ExACpLI.pm plugin with the new pLI scores from gnomad: https://storage.googleapis.com/gnomad-public/release/2.1/ht/constraint/constraint.txt.bgz

However, since the plugin is called ExACpLI, when i supply the gnomad pLI scores the CSQ field in the vcf header will say "ExACpLI", which is not true. Since, the plugin allows other values_file than ExACs would it not be more appropriate to rename to a more generic "pLI.pm" or allow to rename the filed name in the CSQ.

[at7]

Thank you for the feedback. I agree it is a good idea to have a more general name for the plugin. We will look into this for the next release. You could edit the plugin by editing the header line to just pLI: https://github.com/Ensembl/VEP_plugins/blob/release/94/ExACpLI.pm#L119 in the meantime.

[at7]

If you are going to edit the file you also need to change this line: https://github.com/Ensembl/VEP_plugins/blob/release/94/ExACpLI.pm#L130 Change ExACpLI to pLI

[henrikstranneheim]

Ok, Thx! I will do that in meantime.

Will you add support to annotate the pLI per transcript as well, which seem to be supported with the new constraint file from gnomad?

[at7]

Annotating the pLI per transcript is more tricky. But we will definitely look into ways of adding this in future releases.

[henrikstranneheim]

Great! Thx!

[olaaustine]

Hi @henrikstranneheim,
We have generalised the ExACpLI.pm for the next release.
Thank you very much.
Please do open another ticket if you have any issue.
Thank you,
Ola.