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limix / pandas-plink

PLINK reader for Python.
MIT License
78 stars 18 forks source link

reading plink2 format? #13

Open liangyy opened 4 years ago

liangyy commented 4 years ago

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 commented 4 years ago

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

liangyy commented 4 years ago

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

tongqiu-jia commented 2 years ago

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 commented 2 years ago

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