Question: snp annotation using BiomaRt
0
gravatar for Huichen03
17 months ago by
Huichen0310
Huichen0310 wrote:

Hi,

I want to get the gene names from 2400000 snps using BiomaRt in R. But since the snps size is huge, I could not get the result of these snps' annotation for one time. Do you guys have any other suggestions?

Thank you in advance!

snp biomart R gene • 676 views
ADD COMMENTlink modified 17 months ago by Emily_Ensembl19k • written 17 months ago by Huichen0310
2

And it has to be biomaRt in R? Because for example VEP would be the most commonly used tool for snp annotation from Ensembl.

Also, it's not clear in which format your data is, please add an example to your post.

ADD REPLYlink written 17 months ago by WouterDeCoster41k

Possible duplicate, related posts:

Snp Annotation Tool

ADD REPLYlink written 17 months ago by zx87548.2k
4
gravatar for Emily_Ensembl
17 months ago by
Emily_Ensembl19k
EMBL-EBI
Emily_Ensembl19k wrote:

As Wouter says, BioMart is not really a suitable tool for this as it cannot handle that much data. The Variant Effect Predictor (or VEP) can, however take millions of variants and output for you which genes they hit and what effects they have. It will also allow you to filter your list by consequences, frequency, gene names etc, so that you can prioritise variants for further study. For your number of variants I would recommend using the standalone script with a cache, all of which is documented.

ADD COMMENTlink written 17 months ago by Emily_Ensembl19k
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