umlauts problem

[Setss Provider]

I just noticed that plink and plink2 --remove command ignored the participants with umlauts. I imagine this doesn't come up often, but I wanted to flag it. Respectfully

[Chris Chang]

0. Always provide .log file(s) when reporting a problem.

1. In this case, it sounds like there was a subtle DIFFERENCE between the IDs in your —remove file and the IDs in your .fam file, i.e. plink and plink2 are doing the right thing, you are misusing them, and there’s nothing to flag.  If this was not actually the case, please provide a fileset (could contain just one variant) which allows someone else to replicate what you’re seeing.

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[Setss Provider]

Sent you a direct message with my inputs.  Looking forward to learning how i did it wrong.

Thank you

[Chris Chang]

For the mismatching sample IDs, if you look at the raw byte sequence for the o-umlaut character in your --remove file (xxd provides one way to do this), you will see that it's different from the o-umlaut byte sequence used in your .fam file.  Many programs, not just plink/plink2, will not treat these as equal.

You should avoid using such special characters if you don't know how to encode them in a consistent manner.

[Setss Provider]

Thank you. This is very helpful.

Sent from my iPhone

On Aug 19, 2025, at 21:03, Chris Chang <chrch...@gmail.com> wrote: