Question: Is SNPeff still the standard for variant effect prediction?
gravatar for Lauren
8 months ago by
Lauren20 wrote:

I'm kind of new to this space-- a friend of mine says he uses SNPeff for all his exome annotations, and he doesn't know of any other popular tools for this purpose.

I'm annotating some human exomes and I am curious about what else is out there. A search gave me a lot of answers, but I don't know which are popular in the community. Are there gaps the SNPeff leaves that other effect predictors fill? Thank you so much for reading my post!

variant snpeff annotation exome • 363 views
ADD COMMENTlink modified 8 months ago by Samuel Brady230 • written 8 months ago by Lauren20

SnpEff is good also try VEP

ADD REPLYlink written 8 months ago by Medhat7.4k
gravatar for Samuel Brady
8 months ago by
Samuel Brady230
Samuel Brady230 wrote:

The tools I hear used most frequently are SnpEff, VEP, and Annovar. This paper (Table 1) shows a comparison of the three tools.

SnpEff tends to be robust and I personally use it the most. Remarkably, SnpEff can effectively annotate even structural variants and long indels, in addition to traditional smaller variants. I've used Annovar once or twice but strange bugs crop up here and there; however the developer of it maintains it well and offers a lot of documentation. VEP seems quite popular, but I personally have the least experience with this one.

ADD COMMENTlink modified 8 months ago • written 8 months ago by Samuel Brady230
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