PhylogicNDT
PhylogicNDT Modules
PhylogicNDT has 6 modules that can be used to analyze tumor evolution:
- Cluster
- BuildTree
- GrowthKinetics
- SinglePatientTiming
- LeagueModel
- PhylogicSim
To determine the phylogenetic relationship between tumor subclones, we only need to use the Cluster and BuildTree modules.
Cluster
When running the Cluster module, I prefer to use the sif file option. The command line code is much cleaner, and the format provides a much more organized way to keep track of your input files and values.
Sif files have 4 required columns, and 1 optional column:
sample_id: the ID of each sample from the patient
maf_fn: a truncated version of the MAF file with additional CCF information
seg_fn (optional): a truncated version of allelic seg calls (from FACETS or ABSOLUTE)
purity: the purity of each tumor sample from the patient (from FACETS or ABSOLUTE)
timepoint: if temporal ordered by biopsy time, if spatial then arbitrary
Generating the maf_fn file
Generating the sif file
Only a patient ID and the sif file are required to run the Cluster module:
./PhylogicNDT.py Cluster -i Patient_ID -sif Patient.sif
BuildTree
The BuildTree inputs are just a subset of the outputs from the Cluster module:
./PhylogicNDT.py BuildTree -i Patient_ID -sif Patient.sif -m mutation_ccf_file -c cluster_ccf_file
Again, we need to proide the patient ID and the sif file. A description of the mutation CCF file and cluster CFF file output by the cluster module are described below.
mutation_ccf_file: This file contains the cluster assignment of each mutation in the MAF in the maf_fn file.
cluster_ccf_file: This file contains CCF information on each cluster, such as the average CCF of mutations in the cluster and the probability distribution of the cluster CCF.