how to make individual list file when extracting on plink?

Question

[nayeona.hi]

I made individual list file like this:

N2002620115
N2002774440
N2002570297
N2002487409
N2002348348

And used commands

--bfile data --keep ind_list.txt --make-bed --out

According to plink web site tutorial, it must have paired columns - Family ID and Individual ID. I made one column file and two columns file but all failed.

Reading individuals to keep [ data/ind_list.txt ] ...
ERROR: Problem with line:
N2002620115

on my plink screen.

How can I fix it?

Answer 1

[zx8754]

ind_list.txt should have 2 columns FID and IID (FamilyID, IndividualID).

https://www.cog-genomics.org/plink/1.9/filter

--keep accepts a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column, and removes all unlisted samples from the current analysis. --remove does the same for all listed samples.

If we don't have FamilyIDs then just paste the file to make both IDs same:

paste ind_list.txt ind_list.txt > ind_list_new.txt