I would like to use the SnpSift dbNSFP tool to annotate some vcf files.
The description for the tool highlights that pre build versions of the database are available on the SnpSift website, which I did find on the page, https://pcingola.github.io/SnpEff/ss_dbnsfp/.
I have attempted to import the GRCh38 database to galaxy but the download connection keeps being cut off.
Has anyone successfully imported this database to galaxy? Is it available somewhere else?
Try getting the data from here instead: Index of /WGSAdownload/resources/dbNSFP/
Read this file: dbNSFP4.1c.readme.txt – it explains the contents of each file in the directory so you can choose the one you need.
Capture the link for the data you want to use and paste it into the Upload tool. The tool form help explains how to label the data (“datatype”) for the Galaxy wrapped version to recognize the data as an appropriate input.
Note: This data is for hg38 only. There are other ways to get/filter the full data at the website you referenced, but all that prep would be done on the command line first, then the proper filtered result/format loaded up to Galaxy. The exact instructions are on that website - although it doesn’t seem like you’ll need to do that and can instead use the pre-built data linked above, which is far simpler, smaller, and is designed to work within Galaxy.
Hope that helps!
Thanks, I shall try that.