Convert 4 million SNPs' positions to rsID

Question

[Weiqiong]

I have a list of SNPs of the form chromesome:position and I want convert them to rsIDs. I tried Biomart package in R but it was too slow, it will take forever to convert 4 million SNPs. I believe it is possible to download the GRCh37 data and do the job locally instead of requesting information from Ensembl. Does anyone know which is the correct dataset to download and which software I should use? I've download some dataset but they were not the right one, if you can provide a link that will be very helpful.

[Kevin Blighe]

Cross-posted: https://support.bioconductor.org/p/9142285/

[German.M.Demidov]

Search dbSNP for hg19 based coordinates

[Weiqiong]

Thanks a lot. Very helpful.

[cpad0112]

intersect bed with vcf

[Weiqiong]

I've downloaded the VCF file from the following link, is it the correct one to use? Thanks for your help.

https://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/

[cpad0112]

You need to know which build was used in generating your list of SNPs. Accordingly, you need to download dbSNP vcf.

Answer 1

[ning]

ANNOVAR provides an database named "avsnp" for this purpose. More details and a relevant discussion:

http://annovar.openbioinformatics.org/articles/dbSNP/

[Weiqiong]

I'll try to explore it. Thanks a lot for the help.