--pgenPrefix=PGENPREFIX: not for the actual PLINK PGEN file❓

[jielab]

Hi, there:

I use the following script to run SAIGE step 2.

    Rscript software/SAIGE/extdata/step2_SPAtests.R --nThreads=40 \
                --pgenPrefix=/work/sph-huangj/data/ukb/imp/chr22 \
                --GMMATmodelFile=bmi.rda --varianceRatioFile=bmi.varianceRatio.txt \
                --SAIGEOutputFile=bmi.chr22.txt

There is no error message but the output file is empty. Then I checked and found the following message:
--pgenPrefix=PGENPREFIX Path to a file containing genome regions to be included from the dosage file. The file contains three columns for chromosome, start, and end respectively with no header. Note for vcf and sav files, only the first line in the file will be used.

What 😮 ❗ PGENPREFIX is NOT the actual plink PGEN file, but a 3 column text file for chromosome, start, and end？

I realize that SAIGE does NOT actually support PGEN file yet. I have to use --bgenFile option.

Your clarification would be appreciated.

Best regards,
Jie