VEP won't use my CyVerse URLs

Question

[Charlie2]

Hi, I really hope it's true that no question is too trivial or newbie...

I want to use the web version of Variant Effect Predictor with a large vcf. The file is too big to upload directly, so I have stored a copy in CyVerse. The vcf.gz and vcf.gz.tbi (with same name) are in the same folder and I can generate a url that works fine in UCSC genome browser, but when I try with VEP I get a Bad Gateway error. A smaller file works ok, it's only the large one it doesn't like.

Any idea what I need to do?

Answer 1

[Kevin Blighe]

There are undoubtedly limits on both file size and number of variants, i.e., in order to prevent users with large data from clogging the server.

You could divide your file up by chromosome and then annotate each separately..

You coul also download VEP locally and install all necessary databases locally, too, and then run there without limit. It is easy to do, if you have enough disk space to download all necessary files.

Kevin