Associating SNP and GENE

Question

Assuming I have SNPs data using hg19, how can I know which SNP belongs into which Gene?

The data looks like:

chr10_103577643
chr10_124712463

and so on.

I want to add a column of Gene, which would tell to which Gene the SNP belongs. The file is not a VCF file but a Txt file.

Please [edit] your question and show us an example of your data. What do you have? A list of rsIDs? A VCF file? Some other format? How many SNPs? — terdon, Jul 09 '18 at 08:22

score 3 · Answer 1 · answered Jul 09 '18 at 07:47

3

answered Jul 09 '18 at 07:47

Emily_Ensembl

Please don't just post links as answers. It would be great if you could add a short explanation of what VEP is, how to use it etc. Otherwise, this is really a comment and not an answer and would become useless in the (admittedly unlikely) case where the VEP were to be discontinued or its URL changed. For instance, pasting chr10_103577643 into VEP doesn't work, so you could explain what format the data would have to be in. – terdon Jul 15 '18 at 13:02

score 2 · Answer 2 · answered Jul 09 '18 at 08:21

2

You can use snpEff or snpSIFT java annotator also for hg19.

answered Jul 09 '18 at 08:21

Andrea Spinelli

Please don't just post links as answers. It would be great if you could add a short explanation of these tools do, how to use them etc. Otherwise, this is really a comment and not an answer and would become useless if the tools were to be discontinued or their URLs changed. – terdon Jul 15 '18 at 13:03

2 Answers2