Christopher Chang

Oh, sorry, I thought you were referring to e.g. chrX/chrY/chrM. The PgrGetDp() function in pgenlib_read.h is the simplest one that can return biallelic phased dosages.

Have you tried installing the libatlas-dev and libatlas-base-dev packages, which the documentation mentions as necessary for Ubuntu?

Ok, try replacing "-lcblas -latlas" in the Makefile with "-lsatlas". I just tried starting up a new EC2 instance with a CentOS 7.9 AMI, and that did the trick there.

Something along these lines will be supported by the plink 2.0 --clump implementation, but that's still some time away (merge is a higher priority...).

This is now implemented.

The main issue here is that covar.1 is on a wildly different scale (never exceeding +/- 0.00001) than your other covariates (which have variance close to 1). plink2's current implementation...

The temporary solution was implemented on 22 Jan 2019. A better solution is for plink2 to automatically perform variance-standardization, and then convert beta/OR/SE/CI back to the original units in the...

Okay, I will test this, and include the change in the next release if the results look good.

Changed in 9df631b .

plink 1.9 is updated much less frequently than 2.0, but this change may be backported during the next update.