Understanding the workflow

[scienception]

I wanted to know if you had any documentation on the workflow of this software package. And more specifically, in which script are the PGS computed from the weights and dosage?

Thanks!

[smlmbrt]

Some of that information will be in the results/pipeline_info directory, specifically the image of the DAG for your data. The actual scoring is done with the PLINK2_SCORE module which uses plink.

[scienception]

You don't use "thresholding" in your method? (I didn't see the --q-score-range flag). I guess my question is whether this is the C+T method or another one.

[smlmbrt]

No, the pipeline is meant to calculate final PGS (lists of variants and weights). We consider p-value thresholding to be more in the arena of PGS development (for which other tools are optimised).