--hwe flag does not allow p=1 even when specifying k

[Kristen]

Hello,

I am attempting to QC some genetic data using Plink v2.0.0-a.6.9LM. I am trying to use the new --hwe flag options that reflect the recommendations of Greer et al, 2025 (https://doi.org/10.1101/2024.02.07.24301951). (This is the paper the Plink documentation refers to when explaining the new --hwe threshold)

The Greer paper recommends a p-value cutoff of 1e-(n/1000) where n is sample size. In Plink2, the --hwe flag implements this with --hwe <p> [k], which the documentation says will be used to calculate a p-value of p·10^-nk. So if I understand correctly, the way to get the 1e-(n/1000) recommended in the Greer paper (eg. 1·10^-n*0.001) would be with the option --hwe 1 0.001

But when I try using the --hwe flag with those options, I get the error message "Error: Invalid --hwe threshold '1' (must be in [0, 1))."

I tried the latest development build (dated August 17, PLINK v2.0.0-a.7LM) and it still gives me the same error message when using "--hwe 1 0.001".

Is this a bug, or am I misunderstanding what options I need to supply to the --hwe flag to use the threshold recommended by the Greer paper?

Thank you,

Kristen

[Chris Chang]

For now, you can use something like 0.999999.  I will try to post a patch tonight allowing 1.

--
You received this message because you are subscribed to the Google Groups "plink2-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to plink2-users...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/plink2-users/10f13dd6-0c36-4150-b41c-d8d1a313bbbbn%40googlegroups.com.

[Kristen]

Wow, that's a fast response -- thank you!!

Kristen