How to annotate VCF files using SnpSift Annotate and dbSNPs?

Is there any way where I can upload my VCF files (myvcf.vcf) and annotate the rsid of dbSNPs?

I understand I should use SnpSift Annotate and I need the VCF File with ID field annotated (such as dbSNP.vcf). Is it possible that I don’t have to upload this file and can access remotely via FTP? I am not sure how to do this. I am looking for dbSNPs for hg19 genome.

I am trying to do this in the online version of Galaxy.
Thank you.

Hi @anchor,
no I don’t think there is currently a way around uploading the file to a history of yours at least once.

If you need to do this for more than once it may be convenient to maintain a dedicated “resource” files history, from which you just drag the dataset over to each analysis history. This way, as explained in Galaxy Community Hub - Galaxy Community Hub, the file will be counted in your storage quota only once.

In the long run, this tool should be extended to work also with preinstalled annotation data on the server. I’ll give this some thought.

1 Like

Thank you for your reply. I was able to import data from the NCBI FTP server directly to Galaxy without having to download it to my laptop, which was useful. Adding the annotations on the server would be a nice addition, though. Thanks!

1 Like