How to read PAR variants in chr23 from .bgen file?

Question

[David]

Hi

I want to view how my .bgen is formatted (dosage and other stuff) for PAR and non-PAR variants in chromosome 23. I have the index file and the sample file as well. would you please help me?

Answer 1

[carlk]

David, if you're comfortable with Python, please take a look at the bgen-reader package and see if it might be useful for you. I'm a co-author of the program and am available to help with specific questions and problems.

-- Carl

Carl Kadie, Ph.D. (computer science), FaST-LMM & PySnpTools Team, (Microsoft Research, retired) [e-mail]