Obtaining The Snp Rs Number With The Chromosomal Position

Question

[Sheila]

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????

Answer 1

[Ashutosh Pandey]

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

Get rs number based on position

Answer 2

[JC]

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.

Answer 3

[hsiaoyi0504]

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.

[heqianchange]

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

[krassowski.michal]

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