--freqx doesn't work with --family

[JMR JMR]

Hi,

I have been trying to get stratified genotype counts per family ID using the --freqx option together with --family command. It doesn't work, whereas if I only use --freq + --family it does...

Is there a way to achieve what I want?

Thank you,

Javier

[Christopher Chang]

This isn't directly supported by plink; sorry about the inconvenience.  (Defining special cluster-stratified formats for every output file type, as was done with --freq, becomes impractical pretty quickly.) You'll want to write a short script which calls plink one time per family, with --family + --keep-cluster-names [FID].