Using SigProfilerSimulator - Input

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This section describes SigProfilerSimulator's main function and all available parameters.

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Function

The main function in SigProfilerSimulator is SigProfilerSimulator. It randomizes the position of each somatic mutation across the genome while preserving the sequence context, transcriptional strand bias, and chromosomal mutational burden of the input data.

Input files

SigProfilerSimulator accepts four input file formats:

• VCF — one file per sample.
• MAF — standard Mutation Annotation Format file.
• Simple text file — tab-delimited plain text format as described in SigProfilerMatrixGenerator.
• ICGC Format — ICGC simple somatic mutation format.

Input files must be placed in an input/ subdirectory within the project folder.

Running the function

First, start a Python interactive shell and import SigProfilerSimulator:

$ python
>>> from SigProfilerSimulator import SigProfilerSimulator as sigSim

Then call the function with the required parameters:

>>> sigSim.SigProfilerSimulator(project, project_path, genome, contexts)

Required parameters

Parameter	Variable Type	Parameter Description
project	String	Unique name for the given project
project_path	String	Path to the project directory. The input/ subfolder containing the mutation files must exist within this path
genome	String	Reference genome to use. Must be installed using SigProfilerMatrixGenerator. Supported genomes: GRCh37, GRCh38, mm9, mm10, rn6, yeast
contexts	List of Strings	Mutational contexts to simulate. Must be provided as a list (e.g., ["96"], ["96", "ID"]). See the full list of supported contexts below

Optional parameters

Parameter	Variable Type	Parameter Description
simulations	Integer	Number of simulations to generate. Default: 1
exome	Boolean	Restrict simulations to exome regions. Default: None (whole genome)
chrom_based	Boolean	Normalize mutation burden on a per-chromosome basis. Recommended when using the output as background model for SigProfilerClusters. Default: False
gender	String	Determines whether the Y chromosome is included. Accepted values: "female" (default, Y excluded), "male" (Y included)
bed_file	String	Path to a BED file to restrict simulations to user-defined genomic regions. Default: None
vcf	Boolean	Output simulated mutations as VCF files. When False, output is in MAF format. Default: False
seqInfo	Boolean	Save the sequence context information for each simulated mutation. Default: False
seed_file	String	Path to a file containing seeds for reproducible simulations. Default: None
noisePoisson	Boolean	Add Poisson-distributed noise to the simulated mutations. Default: False
noiseUniform	Float	Add uniform noise to the simulated mutations. Default: 0
spacing	Integer	Minimum spacing (in bp) enforced between simulated mutations. Default: 1
cushion	Integer	Cushion (in bp) around the edges of BED file regions within which mutations will not be placed. Default: 100
overlap	Boolean	Allow simulated mutations to overlap. Default: False
updating	Boolean	Update mutation types during simulation. Default: False
region	String	Restrict simulations to a single chromosome (e.g., "1"). Default: None
mask	String	Path to a mask file to exclude specific genomic regions from simulations. Default: None

Supported contexts

Mutation type	Accepted context values
Single Base Substitutions (SBS)	"6", "24", "96", "288", "384", "1536", "6144"
Insertions and Deletions (ID)	"ID", "ID415"
Double Base Substitutions (DBS)	"DBS", "DBS186"