Rename Plink SNPs to their dbSNP rs#

plink_dbsnp.md

Rename plink SNPs to their dbSNP rs id

Download a dbSNP database from the UCSC as a CSV file: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/

For example:

wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp137Common.txt.gz

Note that the chromStart column values are 0-based.

Rewrite all SNP names in your plink .bim file to the corresponding dbSNP rs#. As long as you keep the order intact, all should be fine.

Have you got a script to do this? or is this just a note?
Thank you in advance!

Hi @Heuertje, sorry for not seeing your comment, GitHub doesn't send notifications for Gist comments...

I used something very simple like this:

#!/usr/bin/env python

import sys

snps = {'snp_%s_%s' % (e[0][3:], e[1]): e[2] for e in
        (l.strip().split() for l in open(sys.argv[1]))}

bim = (l.strip().split() for l in open(sys.argv[2]))
new = open(sys.argv[3], 'w')

for e in bim:
    e[1] = snps.get(e[1], e[1])
    new.write('\t'.join(e) + '\n')

new.close()
bim.close()

Use like this if saved as add_snps.py:

python add_snps.py snp137Common.txt original.bim new.bim