Information loss in .bgen to .bed conversion

Question

[rbpz]

I have a .bgen file of imputed genotyping calls (plus corresponding .sample file), and I have converted the file to .bed format for exploration in R. I converted the file using PLINK --make-bed, read the .bed file into R and ended up with a gene dosage file with 0,1,2, or NAs. In another attempt I tried to convert the .bgen file to .gen and read the .gen file to R. The resulting dosage file is a file with 0,1,2, and non-integer values between 0 and 2 (which I assume are the imputed values).

So my question is: is information lost when converting the files into .bed files? Are imputed non-integer values possible in .bed files? I have read the original .bed file documentation but am still quite confused on this.

Many thanks!

[MS]

Did you manage to sort this? See whether --hard-call-threshold helps?