By default, all BED files are SNP-major mode

[richelbilderbeek]

From https://zzz.bwh.harvard.edu/plink/binary.shtml:

I quote:

By default, all BED files are SNP-major mode (as is the example below).

[richelbilderbeek]

From chrchang/plink-ng#195, I got the reply:

The underlying file is variant-major. Individual library functions may perform transposition; you need to look at their documentation.

I assume that means rows are SNPs for .pgen files.

[richelbilderbeek]

As .pgen can read .bed files, I think .pgen and genio should give the same results. Would they disagree, I stick to .pgen as I feel Cheng is (even?) closer to knowing the official standards.