Hello!

I am using Loftee in my VEP pipeline and after some fights with my code everything works now, but the splice site annotations...meaning that I dont get them. There is no error at all, but my vcf files do not contain a single "NON_ACCEPTOR_DISRUPTING" or similar annotation.

Here you can find the relevant part of my code:

--plugin LoF,loftee_path:/home/myname/documents/vep_plugins/loftee,human_ancestor_fa:/home/myname/documents/vep_plugins/loftee/human_ancestor.fa.gz,conservation_file:/home/myname/documents/vep_plugins/loftee/phylocsf_gerp.sql

Any suggestions?

Many thanks in advance!