Alternative to VEP.
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3.2 years ago
joselu ▴ 110

Hi. Variant effect predictor (VEP) does not let me load files larger than 50 Mb. What other program can I use to annotate variants in a larger file? Thank you.

snp VEP • 1.9k views
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Hello,

have you tried searching the web?

fin swimmer

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One vote for SnpEff. The best thing of it is that you could supply your annotations in GFF3 format.

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+1. I would make this comment an answer. Besides, VEP can be run on multiple cores and it doesn't take long to annotate hundreds of thousands of variants.

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Sorry @dariober, wanted to move my comment and instead moved yours. That is why it is now a comment on the toplevel.

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3.2 years ago
ATpoint 55k

Download VEP and run via the command line. It takes VCF files of any size, offering multithreading (forking) and plenty of options to customize the annotation (the Web version does as well of course). It can be installed by conda to save you from getting all the dependencies and perl extensions manually.

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3.2 years ago

SnpEff is probably the other most comprehensive one. Though as @ATpoint said, you can also just run VEP from the command line (SnpEff must be run from the command line anyway, but it has more regulatory annotations than VEP if you're interested in non-coding variants).

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3.2 years ago
Carlos Borroto ★ 2.0k

I recently started playing with Jannovar and I'm pleasantly surprised how easy it has been to get up and running with it. Highly recommend giving it a try.

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