How much accuracy do you get?
Probability values in BGEN are stored to at least 4 decimal places in BGEN v1.1, or to within 1/(pow(2,b)-1), where b is the number of bits used, in BGEN v1.2. This gives the following table
|Number of bits||Probabilities accurate to within||Decimal places of accuracy|
How much accuracy do you need?
The following graphs depict a comparison of -log10 P-values for an association test conducted using an imputed GEN file (probabilities stored to about 3 decimal places of accuracy) versus the same data converted to BGEN v1.2 at different precisions. At 8 bits there's a maximum discrepancy of around 0.03 in the -log10( pvalues ). (The data here represents imputed genotypes at 48,000 and a simulated case/control trait. Only SNPs with a minor allele count of 100, i.e. MAF > 0.1% were tested; no IMPUTE info threshhold was applied.