Parameter	Description
Input/output and display options
-i <arg>	Input file path (required)
-o <arg>	Output file path where the results should be written
-cp	Input data represents cell prevalence (CP) values (as opposed to default VAF values)
-n,−normal <arg>	Normal sample column id in the list of samples, 0-based (e.g. 0 is the first column) (required*)
-clustersFile <arg>	SSNV clusters file path
-s,−save <arg>	Maximum number of output trees to save, if any (default: 1)
-showNetwork,−net	Display the constraint network
-showTree,−tree <arg>	Display the top ranking lineage tree(s) (default: 0)
-color	Enable lineage tree visualization in color mode
-dot	Enable DOT file export of the top-scoring tree for Graphviz visualization (saved by default to: input file with suffix.dot)
-v,−verbose	Verbose mode, prints more information about each step of the algorithm
SSNV filtering and calling
-maxVAFAbsent,−absent <arg>	Maximum VAF to consider an SSNV as robustly absent from a sample (required*)
-minVAFPresent,−present <arg>	Minimum VAF to consider an SSNV as robustly present in a sample (required*)
-maxVAFValid <arg>	Maximum allowed VAF in a sample (default: 0.6)
-minProfileSupport <arg>	Minimum number of robust SSNVs required for a group presence-absence profile to be labeled robust during SNV calling: SNVs from non-robust groups can be re-assigned to existing robust groups (default: 2)
SSNV clustering
-maxClusterDist <arg>	Maximum mean VAF difference on average per sample up to which two SSNV clusters can be collapsed (default: 0.2)
-minClusterSize <arg>	Minimum number of SSNVs required per cluster (default: 2)
-minPrivateClusterSize <arg>	Minimum number of SSNVs required for a private cluster (i.e. with SSNVs occurring only in one sample) (default: 1)
Constraint network construction and tree search
-e <arg>	VAF error margin (default: 0.1)
-minRobustNodeSupport <arg>	Minimum number of robust SSNVs required for a node to be labeled robust during tree search: non-robust nodes can be automatically removed from the network when no valid lineage trees are found (default: 2)
-c,−completeNetwork	Add all possible edges to the constraint network, by default private nodes are connected only to closest level parents and only nodes with no other parents are descendants of root
-nTreeQPCheck <arg>	Number of top-ranking trees on which the QP consistency check is run, we have not seen this check to fail in practice (default: 0, for best performance)

^*

these parameters are required unless the -sampleProfile option is specified