Alamut batch vs free annotation tools like VEP

Question

[quentin54520]

Hello all,

we are considering purchasing an alamut batch license for variant annotation. I would like to have your opinion knowing that it is very expensive, I wonder what it really brings compared to VEP (with the use of plugin to add the effect on the splicing for example).

Answer 1

[Keith]

Hello, I work for a large UK health organisation and we use Alamut batch. I am currently investigating alternative to Alamut batch as It may not be maintained by the company for much longer. Have you manage to find any alternative I would be interested in you opinion.

[quentin54520]

Hello,

I use ensembl variant effect predictor. There are a lot of possible annotations with a lot of plugin. It's quite complicated to install and get all the require data, but then it's a very good tools.

[ED]

VEP is indeed what I would suggest, as it performs just as well (or even better depending on the data) compared to Alamut [1].

I was wondering where you got the information from that the company will not maintain it much longer?

1. Tuteja, S., et al. (2022). "A performance evaluation study: Variant annotation tools - the enigma of clinical next generation sequencing (NGS) based genetic testing." Journal of Pathology Informatics 13.