I have: CHR START END Effect_Allele Ref_Allele columns (hg38)
I want: CHR START END Effect_Allele Ref_Allele RS_ID
I would like to get the SNP rs id using chromosome coordinates, please let me know how I can do this?
Thanks in Advance
You can download dbSNP in VCF format and then use bcftools to extract %CHROM\t%POS\t%REF\t%ALT\t%ID\n as a tab separated file from this VCF. Then, use R (data.table) to join your table to this table withIDs. That's how I'd do it.
Hi, RamRS ~ Thanks for your suggestion. Do you mind sharing the detailed steps and R code?
Yes, I do mind sharing that. Please invest some effort and let us know if you have any specific questions.
Thanks for your advice RamRS. Let me look into that.
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