Get rs ids using chromsome coordinates

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4.3 years 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 • 1.3k views

ADD COMMENT • link updated 4.2 years ago by Biostar 20 • written 4.3 years ago by Mahan ▴ 70

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Download UCSC vcf (hg 38)
Intersect with bcftools or bed tools for ID column. Both bcftools and bedtools, support tab and vcf formats for intersection.

ADD REPLY • link 4.3 years ago by cpad0112 21k

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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.

ADD REPLY • link 4.3 years ago by Ram 44k

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

ADD REPLY • link 4.3 years ago by Mahan ▴ 70

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