Problem to remove subset of patients with plink

Question

[Ginevra]

Hi all, I am trying to remove ID patients from my data and I am using the original PED file for doing that. I create a .txt file with the number of ID family and ID patients that I want to remove put in two columns, but it still doesn't work. The analysis seems to go until the end of the process (creating temporary files) when appears the message saying: Error: duplicates ID.

My command is: $ ./plink --file name --remove IDlist.txt --out subset2 --make-bed

And my IDlist.txt is:

1 2204 
2 1146

So I know I have few duplicates but I don't understand why the presence of duplicates does not allow the removing process.

[Kevin Blighe]

You have encoded the IDlist.txt correctly; however, you should follow-up on the error message. It implies that either your IDlist.txt file or your PED file contains duplicate entries, i.e., the same individual duplicated.

Check the FID and IID of your PED file.

[yx222]

Just wanted to check if this issue has been resolved. I tried to remove duplicate samples by providing PLINK with an ID list that includes all the duplicates I want to remove. However, it still gives me an error message (Error: duplicate IDs) during this process.

[chrchang523]

The first step has to be taken outside of PLINK here. E.g. append "_1" and "_2" to the duplicated IDs in the .ped or .fam file, then mention both in the --remove ID list.