Question: PLINK --update-name command error due to multiple SNPs with same chr:pos but different rs numbers in reference dataset
gravatar for dam4l
4.6 years ago by
dam4l170 wrote:


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!

snp plink • 5.1k views
ADD COMMENTlink modified 4.6 years ago by Maxime Lamontagne2.2k • written 4.6 years ago by dam4l170


I have exactly same problem now. I was wondering, have you figured out this problem to remove the duplicate variant ID?

Thank you.

ADD REPLYlink written 12 months ago by jongyun.jung10
gravatar for Maxime Lamontagne
4.6 years ago by
Maxime Lamontagne2.2k wrote:

PLINK can't choose which rs number to use when you have two rs number at the same position in your --update-name file. You need to modify the --update-name file before using PLINK. You could use R to merge your bim file with the PLINK ref file and when you have duplicate, keep the rs number with the same alleles as your SNP.

ADD COMMENTlink written 4.6 years ago by Maxime Lamontagne2.2k
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