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.