gene annotations based on rsids in ANNOVAR

Question

[HumeMarx]

Hi

I am trying to get gene annotation from rsids. All I have are rsids. Is there anything that would allow me to obtain the genes (if any) these rsids are associated with?

I have tried ANNOVAR but I cannot figure out how to get the information I need when I don't have chromosome positions.

Answer 1

[Steven Lakin]

dbSNP has a batch query system here.

If you want a programmatic way to do it, [BioMart] is a powerful tool you can query against, but there is a bit of a learning curve.

[HumeMarx]

Thanks Steven. Would the gene annotation be in the XML file? Looking at this file, it looks like some sort of a code, and I don't know how to extract information that I am interested in.

[Steven Lakin]

You want to specify the output as BED format (.bed) at the bottom of the submission form and then you can annotate that BED file. UCSC has a web tool where you can download the gene information you need:

Select the relevant gene track you want (RefSeq genes for example), your organism, build, etc.

Then make sure to select "BED - Browser Extensible Data" as the output format. Save it to a file, then use a tool like bedtools to annotate your first BED file with the other BED file.

See this thread for more information: Is There A Easy Way To Find The Gene Annotations For Features In Bed File?