Obtaining The Snp Rs Number With The Chromosomal Position
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8.4 years ago
Sheila ▴ 380

This question is similar to this one (Get rs number based on position).

I have a text file with SNPs in the chr:position format

 10:71086
 10:72876
 10:75794

I was wondering if there is an R package (or perhaps one in Bioconductor) that can take these as input values and provide the SNP rs number associate with them????

r snps bioconductor • 37k views
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8.4 years ago

I think JC has already pointed out a nice resource. The other option would be

Get rs number based on position

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8.4 years ago
JC 12k

It's not in R, but Kaviar (http://db.systemsbiology.net/kaviar/) can give you the RS information using the coordinates and can be accessed locally or remotely.

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2.9 years ago
hsiaoyi0504 ▴ 60

I would like to share another approach. Using EDirect (https://dataguide.nlm.nih.gov/edirect/install.html).

Then you can get the result by running following command:

esearch -db snp -query chr_id[CHR] AND organism[ORGN] AND chr_pos[CPOS]

(modify chr_id, organism, chr_pos to fit your application).

For python, take a look of this function I wrote before https://github.com/hsiaoyi0504/bcinfo/blob/546c54c2f72febd361da59e18b9901591837f826/bcinfo/search.py#L5.

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The first link is unaviable. Can you share this link again? Many thanks.

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Here is another Python wrapper for easy handling of the searches, but without the need to install edirect: https://github.com/krassowski/easy-entrez#example-obtaining-the-snp-rs-id-number-from-chromosomal-position

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