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Convert 4 million SNPs' positions to rsID

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.

snps rsid genomes ensembl vcf
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updated by cpad0112 cpad0112 • written by Weiqiong • Weiqiong

Thanks a lot. Very helpful.

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written by Weiqiong • Weiqiong

intersect bed with vcf

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written by cpad0112 cpad0112

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

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written by cpad0112 cpad0112

1 answer

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

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

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written by ning • ning

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

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written by Weiqiong • Weiqiong

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