The CHISEL command chisel-cloning.py runs the CHISEL pipeline starting from the already estimated allele- and haplotype-specific copy numbers.
To do this, this command requires to have the folder calls with the files and formats described here.
This command is particularly useful if the user would like to re-run the CHISEL's inference of tumor clones to adapt to datasets with particularly high levels of noise and variance.
Examples of usage of this command for QC is described here.