[ensembl-dev] VEP dbNSFP error

[Anja Thormann]

Dear Abhishek,

could you please run tabix -H dbNSFP4.0b2a.txt.gz and let me know if it returns the header line starting with #chr  pos(1-based)..? If that is the case could you please let me know who exactly your are running the VEP command together with the dbNSFP plugin command? If the header is returned correctly I’m wondering if the dbNSFP file path is maybe not found correctly by the plugin.

Regards,
Anja

> On 23 May 2019, at 13:53, Abhishek Nag <abhishek at well.ox.ac.uk> wrote:
> 
> Hi,
> 
> I have been trying to use the dbNSFP database to annotate my variants. Currently, I'm trying to use the latest version of the database (v4.0), but I have also tried using the version 3.5. With both versions, I'm getting the following error message whenever I'm trying to run it -
> 
> Failed to instantiate plugin dbNSFP: ERROR: Could not read headers from dbNSFP4.0b2a.txt.gz
> 
> 
> 
> When I zcat the database file, I am able to read the header line, which was obtained from one of the chromosome files, as suggested in the online manual.
> 
> 
> 
> The formatting steps for the database (including tab indexing) seem to have gone fine, so I'm not sure where the problem is. Also, I am being able to use the other VEP Plugins just fine; for now, I'm getting this error messge with only the dbNSFP plugin.
> 
> 
> 
> It would be great if I could have some pointers regarding where the issue might be.  
> 
> 
> Many Thanks
> Abhishek
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