Question: (Closed) How to download database for annotating snps?
0
gravatar for mandecent.gupta
4.2 years ago by
United States
mandecent.gupta0 wrote:

Hi,

I have snp list and i need to annotate them with the following features. 

Downstream

Non Sysnonymous

Synonymous

UTR3

UTR5

Upstream

Intron

Can you pls suggest me tool or database for annotating snps with above features.

 

 

snp • 1.1k views
ADD COMMENTlink modified 4.2 years ago by Pierre Lindenbaum119k • written 4.2 years ago by mandecent.gupta0
1

Hello mandecent.gupta!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

ADD REPLYlink written 4.2 years ago by Pierre Lindenbaum119k

Annovar is good tool but there is no info about annotating snps with synonymous or non synonymous. Also i could not find info on the link as well. 

ADD REPLYlink written 4.2 years ago by mandecent.gupta0
1

When I run ANNOVAR it creates a file with the file extension ".exonic_variant_function". it lists all variants in exons, and the first column reads "nonsynonymous" or "synonymous".

Did you try using the tool at all? Do look at the output files. 

ADD REPLYlink written 4.2 years ago by karl.stamm3.4k

search biostars for SNpEFF or VariantEffectPredictor

ADD REPLYlink written 4.2 years ago by Pierre Lindenbaum119k
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