Help with ukb_gen_sqc_names

[epela]

Hi Ken

I have used your package ukbtools to label the columns in my ukb_sqc_v2.txt file (really helpful, thank you). However, I still end up with those two columns at the start (x1 and x2) which remained unnamed after I run ukb_gen_sqc_names.

This sqc file doesn't appear to have an IID in it anywhere, However, one of the columns that remains unnamed after I use ukb_gen_sqc_names (x2) looks like it could be IIDs. So, I labelled it as such.

However... if I then try to merge the FID column from the .fam file, into the ukb_sqc file, matching on IID, I get only about 98k matched out of 488k. So presumably this unnamed column in the sqc file actually isn't IID? Or at least it doesn't match my IID column in the fam file?

Have you come across this issue? I've sunk about 3 days trying to sort this now.

Cheers!