Using the Tool - SBS, ID, DBS Input

SigProfilerMatrixGenerator generates mutational matrices for Single Base Substitutions (SBS), Insertions/Deletions (ID), and Doublet Base Substitutions (DBS) from input variant files.

Python Usage

From within a Python session, generate matrices as follows:

python3
>>> from SigProfilerMatrixGenerator.scripts import SigProfilerMatrixGeneratorFunc as matGen
>>> matrices = matGen.SigProfilerMatrixGeneratorFunc("test", "GRCh37", "/Users/test/Desktop/test/")

R Usage

From within an R session:

R
> library("reticulate")
> use_python("path_to_your_python3")
> py_config()
> library("SigProfilerMatrixGeneratorR")
> matrices <- SigProfilerMatrixGeneratorR("test", "GRCh37", "/Users/test/Desktop/test/")

Function Arguments

Required Parameters

Parameter	Type	Description	Example
`project`	string	Project name for this instance of matrix generation	`"alexandrov_lab_test_1"`
`genome`	string	Reference genome to use	`"GRCh37"`
`vcfFiles`	string	Full path to the input files folder	`"/Users/test/Desktop/test/"`

Optional Parameters

Parameter	Type	Default	Description
`exome`	boolean	`False`	Downsamples mutational matrices to exome regions
`bed_file`	string	`None`	Path to BED file for custom region downsampling
`chrom_based`	boolean	`False`	Outputs chromosome-based matrices
`plot`	boolean	`False`	Integrates with SigProfilerPlotting for visualizations
`tsb_stat`	boolean	`False`	Outputs transcriptional strand bias test results
`seqInfo`	boolean	`False`	Outputs original mutations with SigProfilerMatrixGenerator classification
`cushion`	integer	`100`	Adds Xbp cushion to exome/bed_file ranges

Note: All string arguments must be surrounded by quotation marks (e.g., "test"), and all boolean arguments must be True or False.

Input File Formats

This tool supports the following input formats:

Format	Description	Example
MAF	Mutation Annotation Format	example.maf
VCF	Variant Call Format (each sample as separate file)	example.vcf
ICGC	ICGC submission format	ICGC docs
Simple text	Tab-delimited text file	See example below

Simple Text File Format

The simple text format requires the following columns: - Sample name - Chromosome - Position - Reference allele - Alternate allele

Output Folder Structure

The final output is divided into three folders:

Input

Contains copies of the user-provided input files.

Logs

Contains error and log files for the submitted job: - sigProfilerMatrixGenerator_[project]_[genome].err - sigProfilerMatrixGenerator_[project]_[genome].out

Output

Contains the following subfolders: - DBS/ - Doublet base substitution matrices - SBS/ - Single base substitution matrices - ID/ - Insertion/deletion matrices - TSB/ - Transcriptional strand bias results - plots/ - Generated visualizations - vcf_files/ - Processed VCF files

File Extensions

Output files have extensions indicating which arguments were passed:

Extension	Description
`.all`	Default - all mutations
`.exome`	Mutations mapped to exome regions (`exome=True`)
`.region`	Mutations mapped to custom BED file regions
`.chrX`	Chromosome-specific mutations (`chrom_based=True`)