Question: Tool for CDS Variants annotation
0
gravatar for misbahabas
2.5 years ago by
misbahabas60
misbahabas60 wrote:

Hy,

Please there is any tool for CDS variants annotation?? I have cds of 2 genes and want to find synonymous and non-synonymous variants.

snp alignment vcf • 943 views
ADD COMMENTlink modified 2.5 years ago by Kevin Blighe56k • written 2.5 years ago by misbahabas60
0
gravatar for Kevin Blighe
2.5 years ago by
Kevin Blighe56k
Kevin Blighe56k wrote:

ANNOVAR

If your project is research only and not for commercial gain, then use ANNOVAR.

I recommend that you devote time to learning how to use ANNOVAR because the developer constantly updates it and acts rapidly on any bugs that are found. Following the Quick Start-up Guide is probably the best place to go first.

Variant effect predictor (VEP)

Another option is Ensembl's Variant Effect Predictor (VEP). I mainly like VEP because it provides consequemces and predictions over all known transcript isoforms, which is useful when you are doing such an analysis. Of much benefit to you with only 2 variants, VEP has an Online Tool that you can use without the requirement to install anything locally.

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Kevin Blighe56k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1134 users visited in the last hour