Question: Alternative to VEP.
0
gravatar for joselu
17 months ago by
joselu100
joselu100 wrote:

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 • 899 views
ADD COMMENTlink modified 17 months ago by Emily_Ensembl20k • written 17 months ago by joselu100
1

Hello,

have you tried searching the web?

fin swimmer

ADD REPLYlink written 17 months ago by finswimmer13k
1

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

ADD REPLYlink written 17 months ago by Vitis2.3k

+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.

ADD REPLYlink written 17 months ago by dariober11k

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

ADD REPLYlink written 17 months ago by ATpoint29k
9
gravatar for ATpoint
17 months ago by
ATpoint29k
Germany
ATpoint29k wrote:

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.

ADD COMMENTlink modified 7 months ago • written 17 months ago by ATpoint29k
3
gravatar for jared.andrews07
17 months ago by
jared.andrews074.9k
St. Louis, MO
jared.andrews074.9k wrote:

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).

ADD COMMENTlink written 17 months ago by jared.andrews074.9k
3
gravatar for Carlos Borroto
17 months ago by
Carlos Borroto1.9k
Washington Metropolitan Area
Carlos Borroto1.9k wrote:

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.

ADD COMMENTlink written 17 months ago by Carlos Borroto1.9k
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