reading plink2 format?

[liangyy]

Hi developer,

Thanks for developing this nice package. I was wondering if we have the plan to support plink2 format in the future.

Thanks!

Yanyu

[horta]

Do you have link to that format? I wasn't aware of that...

[liangyy]

Here is the link https://www.cog-genomics.org/plink/2.0/input#pgen.

[tongqiu-jia]

Being able to read plink2 format would be a great feature to have!
.pgen can encode dosages from imputation, which can be further manipulated with pandas-plink.

[francois-a]

pgenlib can be used to load dosages from pgen files into numpy. A simple wrapper is available here.