Extract variants with same rsid

[Caterina]

I have a few variants with same rsid but multiallelic variants:

1 10690948 rs17035482 C G
1 10690948 rs17035482 C T

How can I use the --extract flag to specify which variant I'd like to keep?

Thanks for your help :)

[Christopher Chang]

You must use something like plink2's --set-all-var-ids flag to first assign these variants unique IDs; otherwise --extract cannot distinguish between these variants.  (--recover-var-ids can be used later when you want to restore rsIDs.)

[Caterina]

Could you please give me an example of the format for set-all-var-ids?

Something like 

CHR:POS:REF:ALT?

[Caterina]

Would that be @:#:\$r:\$a ?

[Christopher Chang]

That should work.