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I have ~500,000 rsids - but want which chromosome each SNP resides on. How can I do this?

MarkerName A1 A2 
rs2326918 a g 
rs7929618 c g 
rs66941928 t c 

I want the chromosome number associated with each MarkerName. So the output would be like this:

MarkerName A1 A2 Chr
rs2326918 a g     6 
rs7929618 c g     6
rs66941928 t c    6

How can i do this?

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    $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Jul 14, 2022 at 13:22
  • $\begingroup$ Thanks for the clarification @workhorse $\endgroup$
    – M__
    Jul 14, 2022 at 14:20
  • $\begingroup$ I'd recommend consulting the RefSNP documentation ncbi.nlm.nih.gov/snp/docs/RefSNP_about $\endgroup$ Jul 14, 2022 at 23:50
  • $\begingroup$ @Workhorse thanks for your question. Please consider upvoting/accepting the answer by NiekdeKlein $\endgroup$
    – M__
    Sep 14, 2023 at 12:14

1 Answer 1

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Download dbsnp VCF file from https://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/. This contains rs IDs and chromosome info (among other info). Can match your rs IDs to the rs IDs in dbsnp VCF, and extract chromosome from there.

See https://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/ for more information on the dbsnp files.

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