Duplicate ID error with update-name flag
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7 weeks ago
geno89 ▴ 10

Hi I am trying to update my SNP ids to rsIDs by using --update-name command but getting the error of " Error: Duplicate ID 'var1'". Why is this happening and How can i remove this error?

plink --bfile b.ff  --update-name ref.txt --make-bed --out test_updateIDs
PLINK v1.90b6.21 64-bit (19 Oct 2020)          www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to test_updateIDs.log.
Options in effect:
  --bfile b.ff
  --make-bed
  --out test_updateIDs
  --update-name ref.txt

96310 MB RAM detected; reserving 48155 MB for main workspace.
Allocated 15236 MB successfully, after larger attempt(s) failed.
517563 variants loaded from .bim file.
1926 people (977 males, 949 females) loaded from .fam.
972 phenotype values loaded from .fam.
Error: Duplicate ID 'var1'.
Chromosome SNP position Plink unix rsid • 197 views
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Presumably because the ID 'var1' occurs multiple times in the .bim file.

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And how can i remove this var1 from my .bim file

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You don't want to remove it - you want to make sure each ID is unique. Personally I would load the .bim file into R and then edit the column to make the identifier unique. If you edit your original question (don't post it in the comments) to include the first 10 or so lines from the bim file, I will write an answer and show you how.

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Entering edit mode
7 weeks ago
zx8754 10k

Here is an R example script to make it unique:

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