Gnomad variant effect columns

[idraktt]

Gnomad variant effect columns

[lgmgeo]

Hi @idraktt,

Actually, these annotation columns are not distributed with AnnotSV.
That's why they are not in the README.

Let's have a look at your install.
Can you run these commands:

ls -l $ANNOTSV/share/AnnotSV/Annotations_Human/Users/*
ls -l $ANNOTSV/share/AnnotSV/Annotations_Human/Users/*/*

Else, do you have any annotation file indicated in your configfile that I can't see in your command line?
The "configfile" can be located:

• in the same directory as your input file
• in the installation directory in $ANNOTSV/etc/AnnotSV/configfile

[idraktt]

Dear @lgmgeo ,

Thank you very much for your quick response.

Someone else added Gnomad Annotations on our HPC cluster to AnnotSV installation. Now it is clear from where they are coming.

[lgmgeo]

Great!