Is GWAS genotype QC to exclude samples with inbreeding coefficient typically applied to only autosomes?
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.
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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
autosomes is enough. if you want to use chrX, that's fine