issues using GDI database

[aminhaghparast]

hi...
I downloaded the GDI_full_10282015.txt from the link "https://annovar.openbioinformatics.org/en/latest/user-guide/download/#user-contributed-datasets" and added manually to humandb folder and wanted to add it to my annotation databases, however, I tried many versions of table_annovar.pl command but I could not find a way to make it work...I am wondering if I need to make any modification on GDI_full_10282015.txt file or there is other way to execute table_annovar.pl . could you please help me out with this issue?

[kaichop]

The GDI is a user-contributed database and it is not in a standard format that ANNOVAR can use (gene, filter, region based annotation). You need to write a script to use it in your analysis since it is a gene-level score not a variant level score. For example, you can take all genes over a specific score threshold and then filter your variants that are annotated as protein-disrupting in that gene.

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On Thu, Sep 30, 2021 at 6:51 AM aminhaghparast ***@***.***> wrote: hi... I downloaded the GDI_full_10282015.txt from the link " https://annovar.openbioinformatics.org/en/latest/user-guide/download/#user-contributed-datasets" and added manually to humandb folder and wanted to add it to my annotation databases, however, I tried many versions of table_annovar.pl command but I could not find a way to make it work...I am wondering if I need to make any modification on GDI_full_10282015.txt file or there is other way to execute table_annovar.pl . could you please help me out with this issue? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#161>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OH7R26UJB4RYEFRP3DUEQ6LLANCNFSM5FCA6B2Q> .