It uses msprime to simulate a lineage tree of single cells in the developing animal, then uses a custom finite sites mutation simulator to add somatic mutations based on COSMIC SBS signatures.
options:
-h, --help show this help message and exit
--cells CELLS Integer. The number of cells in your simulated sample
--reps REPS Integer. Number of simulation replicates
--sequence SEQUENCE Optional: the sequence you would like to simulate mutations on. Leave empty to randomly generate a sequence, or
query a ref genome for a sequence.
--seq_len SEQ_LEN Integer. Length of randomly generated sequence to simulate mutations on.
--new_seq_per_rep Include flag if you want to generate a new random sequence each replicate. Overrides other seq arguments.
--genome GENOME Specify genome to generate random sequence with appropriate GC content. Currently only mm10 is supported
--genome_fasta GENOME_FASTA
Path to indexed fasta to query
--regions REGIONS [REGIONS ...]
region or list of regions (separated by spaces) of provided reference genome to simulate mutations within, in the
following format: chr1:200-300
--growth_model GROWTH_MODEL
currently only exponential is supported
--coalescent_model COALESCENT_MODEL
Model provided to msprime.sim_ancestry
--Ne NE Integery. Population size at time of simulated sampling.
--Mu MU Float. Overall mutation rate. default=2e-6
--sbs_signatures SBS_SIGNATURES [SBS_SIGNATURES ...]
Path or list of paths (separated by spaces) to COSMIC SBS signatures in default tsv format. The two PolE-P286R
signatures (SBS10a and SBS10b) and SBS5 are provided and used by default.
--sbs_weights SBS_WEIGHTS [SBS_WEIGHTS ...]
floats separated by spaces. SBS signature weights, used if multiple signatures provided.
--outdir OUTDIR Directory for outputs. Will be created if it does not exist
--name NAME name for your simulation, will be the prefix of output files.
--save SAVE True or False. Whether to save outputs. Default = True