Gtf File For Watson Snps

Question

[Andrea_Bio]

Hi

In a recent question on this forum I saw a link for gtf file for homo sapiens from ensembl here. Thanks to the use Alex who answered the original question.

I was wondering if it was possible to get anything like this just for watson snps giving the ensembl consequences of each watson snp?

I should point out that ensembl do not currently provide this information but I was wondering if someone else had made this data available.

thanks

Answer 1

[Giulietta - Ensembl Helpdesk]

Hi,

Based on the genomic locations, you can use the Variant Effect Predictor to determine the effect, or consequence(s), of those variations on the Ensembl transcripts. Either use the web interface, or perl API: http://www.ensembl.org/tools.html

An example input and output are here.

Hope this helps.