Is GWAS genotype QC to exclude samples with inbreeding coefficient typically applied to only autosomes?

Question

[curious]

I am read this QC pipeline:

https://sites.google.com/a/broadinstitute.org/ricopili/preimputation-qc#TOC-Technical-Details

They say to exclude samples with heterogeneity F statistic, also known as the inbreeding coefficient +- .2.

This is probably referring to autosomes only right? I would think this cutoff would not work if including sex chromosomes.

My understanding is that plink --het "computes observed and expected autosomal homozygous genotype counts", so I would guess most people probably just use that, unless they are renaming chrs.

[curious]

OP here, probably yes based on this:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5537640/

and this:

http://www.bioinf.wits.ac.za/courses/gwas/OLD/Qc_combined_final.pdf

[Shicheng Guo]

autosomes is enough. if you want to use chrX, that's fine