I have a data file containing autosomal SNPs imputed from the 1000 genomes data. The SNPs in my file are named as chr:pos but I want them to be named by rs number. I downloaded the 1000 genomes phase 1 data from the PLINK resources site, excluded sex chromosomes, and organized the file so that I have 2 colums: chr:pos (column 1) and corresponding rs number (column 2). I then tried to use PLINK --update-name command to update the SNP names in my file:
./plink --bfile my_data --update-name 1000_genomes_chrpos_rs.txt --make-bed --out my_data2
I got back the following error message - Error: Duplicate variant ID '1:2351395' in --update-name file.
In the 1000 genomes file, this (and likely other) chr:pos corresponds to multiple rs numbers. Is there a way to rectify this or modify the PLINK command so that I can change the naming of the SNPs in my data file from chr:pos to rs number?
Thanks so much!