Error: --update-map variant ID '.' appears multiple times in dataset.

[Maria Luisa de Barros Rodrigues]

I'm trying to litfover the SGDP built 2021 data from hg19 to hg 38.
The data is in bcf format, but there is no ID information.
When I try to update the positions with the following command

                 $        plink2 --bfile chr.sgdp.pub.22 --exclude chr.sgdp.pub.22_hg38_unmapped --update-map chr.sgdp.pub.22_hg38_update --export vcf-4.2 --out chr.sgdp.pub.22_hg38

the error appears:

                 Error: --update-map variant ID '.' appears multiple times in dataset.

Is there a way to update the positions in another way?
or is there a way to retrieve the IDs somehow?

[Christopher Chang]

Many plink2 commands only work when variants have unique IDs.  The --set-all-var-ids flag (possibly followed by --rm-dup) provides one straightforward way to ensure this.

[Maria Luisa de Barros Rodrigues]

Thank you! It worked!