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[PLINK] Error: Duplicate ID when running an --update-ids

I am running the following script to update IDs in my PLINK project:

plink \
   --bfile Project1 \
   --update-ids UpdateIDs\
   --make-bed --out /Renamed/Project1

But when I try to run it, I get the following error:

Error: Duplicate ID '009-009 009-009-01'.

Sample file structure for UpdateIDs:

1   GSA_009-009_009-009-01_A01B01   009-009 009-009-01

Which is a tab-separated file containing following columns: old_fid, old_iid, new_fid, new_iid. I've checked the fam file and there are no actual ID duplicates, which is why I'm currently confused...

software-error gwas snp plink
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updated by marcoabbestia • marcoabbestia • written by njofrica • njofrica

Hard to guess without seeing your Project1.fam file and UpdateIDs file.

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written by zx8754 zx8754

2 answers

Your issue lies in your UpdateIDs file. Particularly, you have multiple values for a singular key (assuming a map-like replacement). You can take one of two paths: either prune the excess lines yourself using a Python script (you will have to decide which value you will want to prioritize for each key) or you can use another tool (something like awk) to prune these lines.

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written by ashishjayamohan • ashishjayamohan

Hello, you should remove the space from "009-009 009-009-01". You can use a function like gsub in R to remove it

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written by marcoabbestia • marcoabbestia

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