Question

snp annotation using BiomaRt

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6.6 years ago

Huichen03 ▴ 40

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 R gene bioMart • 2.7k views

ADD COMMENT • link updated 6.6 years ago by Emily 24k • written 6.6 years ago by Huichen03 ▴ 40

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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 REPLY • link 6.6 years ago by WouterDeCoster 47k

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Possible duplicate, related posts:

Snp Annotation Tool

ADD REPLY • link 6.6 years ago by zx8754 12k

score 5 · Answer 1 · 2018-05-04

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.