Question: Error: Duplicate ID '26:42' generated by --set-missing-var-ids.
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gravatar for manubiomed20
9 months ago by
manubiomed2010
manubiomed2010 wrote:

I used the command below to update variant information, but something went wrong, it seems that my vcf has 2 variants in the same position.

 :~/Documentos/PLink_Manu$ 
      plink --file dis-MT --set-missing-var-ids @:# --recode --out dis-MT
       PLINK v1.90b6.10 64-bit (17 Jun 2019)          www.cog-genomics.org/plink/1.9/
        (C) 2005-2019 Shaun Purcell, Christopher Chang   GNU General Public License v3
          Logging to dis-MT.log.
           Options in effect:
              --file dis-MT
              --out dis-MT
              --recode
              --set-missing-var-ids @:#

            20061 MB RAM detected; reserving 10030 MB for main workspace.
            Possibly irregular .ped line.  Restarting scan, assuming multichar alleles.
            .ped scan complete (for binary autoconversion).
            Performing single-pass .bed write (4602 variants, 4513 people).
            --file: dis-MT-temporary.bed + dis-MT-temporary.bim + dis-MT-temporary.fam
            written.
        Error: Duplicate ID '26:42' generated by --set-missing-var-ids.

so I used the following command:

 plink --file dis-MT --set-missing-var-ids @: # [b42] \ $ 1, \ $ 2 --recode --out  dis-MT

but the following error appeared:

Error: The --set-missing-var-ids template string requires exactly one '@' and
one '#'.
For more information, try "plink --help <flag name>" or "plink --help | more".

what should I do?

plink • 236 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by manubiomed2010

Remove all the spaces from the middle of the --set-missing-var-ids argument.

ADD REPLYlink modified 9 months ago by RamRS27k • written 9 months ago by chrchang5236.9k
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