Clicking the Download button downloads a .zip file that contains the files exported from Tapestri Designer. The files at the top level of the .zip file are used to run Tapestri Pipeline. This .zip file should be submitted to BlueBee without any changes.
The .zip file contains a Designer folder. For the hg19 genome, the folder contains four additional files. For the mm10 genome, it contains three files because it does not have a systematic-variants.blacklist file.
All coordinates in the .bed files belong to either the hg19 (GRCh37) or mm10 (GRCm38) genome assemblies.
For more information on the downloaded .zip file, refer to this file.