Any tutorial how to "link" SNPs with genes?

Question

[Roland]

Hi.

I have a reference genome, and I've mapped reads from 100 samples onto the reference genome. I have also identified some SNPs that are of interest. What I want to do now is to find where in the reference genome these SNPs are located, and then find if there are any genes found nearby.

Is there any tutorial on how to do this, that you could recommend me?

Thank you.

[raphael.B]

You can start by annotating your snps using SNPEFF. This will give you information on SNPs falling in or near known genes, with a prediction of their functional impact.

[Roland]

Thank you, I will check it out.

[Pierre Lindenbaum]

I have also identified some SNPs that are of interest

what does it mean ? in the litterature ? in your VCF ?

and then find if there are any genes found nearby.

How To Find Nearest Gene To A Batch Of Snps

How To Map A Snp To A Gene Around +/- 60Kb ?

etc....

[Roland]

what does it mean ? in the litterature ? in your VCF ?

Well, basically I've ran a tool that identifies SNPs that are "under selection".

Thanks for the links!

[dthorbur]

Similar to raphael.B recommendation, an alternative is ENSEMBL's VEP tool. It'll annotated SNPs into classes, infer level of impact, and highlight genes that are hit, but it does require that the species and assembly you used to call SNPs is annotated on ENSEMBL.