Identify individuals with a set of variants

[Shoa Clarke]

I would like to identify all of the individuals who carry a set of variants. I am able to do this one variant at a time with the following command:

> plink2a --pfile pfile_root --snp variant_ID_1 --export A include-alt

This command generates a plink.raw file that allows me to see which individuals carry the variant.

I would like to do the same for a whole list of variants. I have tried this with --extract without success. I create a file containing a list of variants that looks like this:

> cat variant_list.txt

variant_ID_1

variant_ID_2

variant_ID_3

I then run the following command:

> plink2a --pfile pfile_root --extract variant_list.txt --export A include-alt

This produces a plink.raw file that is empty.

I'm guessing that I have misunderstood how --extract is meant to work. Is there a recommended way to get a list of individuals who have a given set of variants (by variant ID), using .pgen/.pvar/.psam files?

Thanks!

[Christopher Chang]

That should work; are you sure the variant IDs match up exactly?