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Get rs ids using chromsome coordinates

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
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updated by Biostar Biostar • written by Mahan Mahan

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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written by Ram Ram

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

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written by Mahan Mahan

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

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written by Ram Ram

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

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written by Mahan Mahan
  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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written by cpad0112 cpad0112

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