Entering edit mode
4.6 years ago
manubiomed20
▴
10
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?
Remove all the spaces from the middle of the
--set-missing-var-ids
argument.