The PAR bed file was mis-specified with -par rather than --par. This issue is addressed here.
Fix output specification if external AF ref bed is not provided, so that users can choose not to perform that annotation
Add PAR BED to reference resources and supply as an input to AnnotateVcf (and single-sample pipeline which runs AnnotateVcf) by default in JSON templates (terra & test)
Update input names for inputs associated with external AF annotation to clarify their purpose (I kept thinking that population was the list of populations in the cohort, but it's actually the populations in the external AF ref bed)
Testing
Validated all WDLs and JSONs with womtool and Terra validation script
Tested without external AF annotation (successful)
Tested with PAR BED input (successful, PAR INFO field added)
Updates
-parrather than--par. This issue is addressed here.populationwas the list of populations in the cohort, but it's actually the populations in the external AF ref bed)Testing