Quick Start Example¶

This section provides a minimal example to get started with SigProfilerSimulator. The following example generates 100 simulations from a VCF input using the GRCh37 reference genome and the SBS-96 context.

Prerequisites¶

This tutorial requires that you have completed all steps in the installation guide, specifically:

Installed SigProfilerSimulator
Downloaded the GRCh37 reference genome using SigProfilerMatrixGenerator

Input data¶

SigProfilerSimulator accepts four input file formats: VCF, MAF, simple text file, and ICGC format. Input files must be placed in an input/ subdirectory within the project folder:

path/to/project/
└── input/
    ├── sample1.vcf
    └── sample2.vcf

Running SigProfilerSimulator¶

Start a Python interactive shell and import SigProfilerSimulator:

$ python
>>> from SigProfilerSimulator import SigProfilerSimulator as sigSim

Run the simulator on your data. Note: Update "path/to/project/" with the actual path to your project directory.

>>> sigSim.SigProfilerSimulator("my_project", "path/to/project/", "GRCh37",
                                 contexts=["96"], simulations=100, chrom_based=True)

After SigProfilerSimulator has finished, the simulated mutation files will be placed in the output/ subdirectory of your project folder, organized by context and simulation number.

Additional Information¶

In the above example, unspecified parameters use their default values. All function arguments are described in detail in the Using the Tool section. For the full list of supported reference genomes, refer to the Supported Genomes section.