Undrestanding BGEN files

Question

[Mazza]

Hi all,

I have worked with Plink format files only and now I am facing some files they are all in .bgen .gen . sample .stats and so on format. I am really confused can anybody tell me how I can find the number of SNPs and Individuals with these files and how to read them? when I less them they are too busy I can not find any thing at all.

Answer 1

[Sam]

You can find the detail information of the bgen format here:

http://www.well.ox.ac.uk/~gav/bgen_format/

Basically, this is a type of dosage data. Unfortunately, the bgen format is in binary. So you will either have to write your own programme or use some external programe to handle them. If all you want is just the number of SNPs and number of individuals and doesn't care much about the dosage, then you can use plink directly https://www.cog-genomics.org/plink/1.9/input#oxford

(If you only want the number of individual, read the .sample file, it will contain all the sample name and their pheontypes)