I have obtained a publicly available GWAS summary data which contain column such as chromosome: position (for SNPs), effect allele, reference allele, beta, se, P-value. I need the rs ID of all the SNPs (around 700000snps). How can I get the rs ID of the given SNPs based on chromosome and position. Any r packages or tools/software?
Your suggestions are highly appreciated!
Thanks
You can try using snpGeneSets package in R for annotation and analysis of GWAS data.
May you find the best answer here:
SNP FAQ Archive from NCBI help manual.
(Batch Query: Retrieving information for a large number of SNPs.)
https://www.ncbi.nlm.nih.gov/books/NBK3848/?term=SNP
If it's less than 700k, I highly recommend UCSC table browser.
However, for that number of SNPs --- in my hands at least --- usually it's easiest to download the 1000genome data set and make a small custom script to match up chr:position to rsid.
Due caution - this is trivial for common single-nucleotide polymorphisms (assuming that's what you have), but becomes seriously difficult for rare stuff and when going into indel land.
I strongly recommend using ANNOVAR. You can not only annotate your variants for functional consequence but you can also get their rsIDs by specifying the filter for avsnp150 (both hg19 and hg38) or the latest version available on ANNOVAR's webpage (https://annovar.openbioinformatics.org/en/latest/user-guide/startup/).
No need to write any scripts but requires a know how to run simple commands on the terminal.
All the best.
hello dear colleague if you have one gene for your study you may retrieved the SNPs with its rsID from db SNPs or ensemble database.
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