Get rs ids using chromsome coordinates
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13 months ago
Mahan ▴ 70

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

rs id Chromosome Coordinates Hg38 • 418 views
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  1. Download UCSC vcf (hg 38)
  2. Intersect with bcftools or bed tools for ID column. Both bcftools and bedtools, support tab and vcf formats for intersection.
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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.

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Hi, RamRS ~ Thanks for your suggestion. Do you mind sharing the detailed steps and R code?

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Yes, I do mind sharing that. Please invest some effort and let us know if you have any specific questions.

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Thanks for your advice RamRS. Let me look into that.

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