Removing duplicate varaints in PLINK

Question

[f-rasmussen]

I have binary plink containing duplicates which I want to remove without removing all of the variants. I therefore use the flag --rm-dupas recommended by plinks website:

[https://www.cog-genomics.org/plink/2.0/filter#rm_dup ][1]

I paste in the command as such:

plink --bfile with_duplicates --rm-dup force-first --make-bed --out without_duplicates

However I get the error message:

Error: Unrecognized flag ('--rm-dup').
For more information, try 'plink --help [flag name]' or 'plink --help | more'.

I have tried to remove the file and mode from the flag, but with same results. The help page doesn't have an entry for this particular flag either. Does anyone know how to fix this issue?

Also, does the --rm-dup remove duplicates based on position or variant ID or both? It doesn't say from the webpage.

Answer 1

[lax]

to my understanding this flag is for plink2. So the following should work after upgrading to plink2.

plink2 --bfile with_duplicates --rm-dup force-first --make-bed --out without_duplicates