diff --git a/Utilities/WDLs/PRSQC.wdl b/Utilities/WDLs/PRSQC.wdl index 476aa3c3c..43826c6a9 100644 --- a/Utilities/WDLs/PRSQC.wdl +++ b/Utilities/WDLs/PRSQC.wdl @@ -10,6 +10,13 @@ workflow PRSQC { File sample_acceptable_range File control_expected_pcs Float margin_control_pcs + # This alphashape is essentially a bounding polygon containing the set of points in the form (PC1, PC2) + # from a training set, such as 1kG. It was generated using the library: https://github.com/bellockk/alphashape + # We have a script that allows generating alphashapes with an arbitrary training set (of valid format), + # which can be found here: https://github.com/broadinstitute/palantir-workflows/blob/main/Utilities/Dockers/Alphashape/generate_alphashape.py + # The main (and pretty much only one besides training data) parameter of interest is "alpha", which determines how tight + # the bounding polygon is. Our default is set at 8.0, which was determined to be a good value experimentally. + # Users who intend to use a training set different than the default (1kG) should be aware of this. File alphashape Boolean manually_passed_control = false }