Running HARE on sex chromosomes?

[ossmith]

From an email to me:

[When running HARE I got a] a warning message. I then checked my gwas_data.txt, removed all lines with X chromosome, reran HARE, and then no warning message showed up.
Does that mean it is recommended to use autosomal GWAS only when using HARE?

[ossmith]

HARE automatically constrains to autosomes when you run on humans. Generally for quality reasons, Y chromosomes aren't analyzed in GWASs. My understanding is that there are sometimes additional considerations for X in the GWASs, but as long as you trust the GWAS QC on the X, it should be ok. The reference genome I provided (UCSC file under 'reference assets') is autosomes only, but you could add sex chromosomes to it (just by downloading them from UCSC and then appending).

I haven't tested whether all of the dependencies (VEP, BioMart, bcftools) will work though, so I will need to add a test for that.