Using the Tool SBS ID DBS Input

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/")

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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.

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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

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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

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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)