Convert 4 million SNPs' positions to rsID
1
2
Entering edit mode
7 months ago
Weiqiong ▴ 20

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 • 884 views
ADD COMMENT
0
Entering edit mode
ADD REPLY
0
Entering edit mode
ADD REPLY
0
Entering edit mode

Thanks a lot. Very helpful.

ADD REPLY
0
Entering edit mode

intersect bed with vcf

ADD REPLY
0
Entering edit mode

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/

ADD REPLY
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
7 months ago
ning ▴ 50

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

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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2126 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6