plink2 --within flag not clustering

[Renée Fonseca]

I was attempting to calculate allele frequencies by population using the --within flag as follows:
plink2 --bfile in_file -allow-no-sex --freq --within populations.txt --out out_file
Analysis ran and output a .afreq file but was lacking any clusters/stratification. I ran the exact same analysis but using plink 1.9 rather than plink 2 as follows:
plink --bfile in_file -allow-no-sex --freq --within populations.txt --out out_file
and the output file (.frq.strat) contained CLST column as expected.
Plink2 doesn't seem to be clustering properly using the --within flag. Additionally the --family flag is not clustering by FID using plink2 (outputs un-clustered .afreq file).

[Christopher Chang]

This is a case where backward-compatibility was deliberately dropped in plink2 because the old behavior was a weird corner-case relative to the rest of plink's design.

The plink2 way to get cluster-stratified statistics is to combine --within/--family with --loop-cats; this generates a separate set of output files for each category. If you prefer what plink 1.x did, it's fine to continue using it; it will continue to be maintained.

[Renée Fonseca]

Thanks for letting me know!