`all_cba.KLEAT.on-target-cleaned.filtered.clustered.csv.gz`

is the clean version of all cleavages used in the analysis after filtering and
clustering. This is likely the version you would like to use.

`all_cba.KLEAT.csv.gz`

is raw cleavage site predictions concatenated from KLEAT outputs of all samples
from the pipeline https://github.com/bcgsc/tasrkleat. If you would like to do
the cleaning and filtering in a different way, you could use this version.