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Published 20 hours ago • verified publisher icon limix

reading plink2 format?

Open liangyy opened this issue 4 years ago • 4 comments

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

liangyy avatar Mar 26 '20 15:03 liangyy

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

horta avatar Apr 20 '20 11:04 horta

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

liangyy avatar Apr 22 '20 11:04 liangyy

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.

tongqiu-jia avatar Apr 20 '22 23:04 tongqiu-jia

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

francois-a avatar Jun 29 '22 05:06 francois-a