ERROR: step2_SPAtests.R ... has B = 16 (not 8)

[luanjianan]

I got an error message in Step2_SPAtests below, where "1:214154719_G_T" is the first SNP's name in my BGEN file. My BGEN file includes only 38 SNPs and are in GP (genotype probabilities) format.
Your help will be appreciated very much.
Jianan

......
450106 samples have been used to fit the glmm null model
variance Ratio is 0.849
487409 sample IDs are found in sample file
[1] 487409 4
[1] "IID" "IndexInModel" "IndexDose.x" "IndexDose.y"
450106 samples were used in fitting the NULL glmm model and are found in sample file
minMAC: 1
minMAF: 1e-04
Minimum MAF of markers to be testd is 1e-04
Analysis started at 1.52e+09 Seconds
no query list is provided
487409 samples are found in the bgen file
38 markers are found in the bgen file
isVariant: TRUE
It is a binary trait
Analyzing 25529 cases and 424577 controls
ERROR: 1:214154719_G_T has B = 16 (not 8)

[joshbTerps]

You need to use 8-bit compression. Run qctool v2 with "-bgen-bits 8"

[luanjianan]

The trick works. Thank you very much joshbTerps.