--check-sex/--impute-sex requires at least one polymorphic X chromosome locus

[Braulio Valencia]

Hi all,

I'm doing QC of my GWAS data and this error message is reported when --check-sex is attempted:

--check-sex/--impute-sex requires at least one polymorphic X chromosome locus

Sorry for bothering with silly questions again.

Kind regards,

Braulio

[Christopher Chang]

You can't use --check-sex on e.g. chr1, since that contains no sex information.

[Braulio Valencia]

Thanks for your reply. For some reason chr 23 and 24 were not label as such in my bim file. Instead chr X and XY are listed. I'm guessing I can replace X and XY as 23 and 24. Is that correct? X=23 and XY=24? or the way around?

Thanks again!

B

[Braulio Valencia]

Sorry, there's an imprecision in my last post. These two chr are listed: Y and XY. 

Y=24

XY=25

But why I can't find a X chr?

[Christopher Chang]

You need to ask the provider of the file.

With that said, plink 1.9 --check-sex has a "y-only" mode which might suffice for your purposes.

[Braulio Valencia]

Awesome, thanks! You're a star!!!

So, what's the script for that?

plink --bfile <file> --check-sex y-only

?

So sorry for being so annoying!

Cheers,

B

[Christopher Chang]

plink --help check-sex

or read the --check-sex online documentation