Using SigProfilerClusters - Output

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This section describes the output files and directories produced by SigProfilerClusters. All results are written under [project_path]/output/, organized into several subdirectories.

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Output Overview

After a successful run, the output directory contains the following subdirectories:

[project_path]/output/
├── clustered/
├── nonClustered/
├── plots/
├── simulations/
└── vcf_files_corrected/

All errors and progress checkpoints are also saved as log files in the project directory:

• SigProfilerClusters_[project]_[genome].err — error log
• SigProfilerClusters_[project]_[genome].out — progress log

clustered/ Directory

Contains the partitioned clustered mutations, organized into subclass subdirectories. Within each subclass folder, one VCF file is saved per sample. The subclasses correspond to the categories described in the Workflow section:

Subclass	Description
DBS/	Doublet base substitutions (2 adjacent SNVs)
MBS/	Multi-base substitutions (3+ adjacent SNVs)
omikli/	Localized clustered events (2–3 SNVs)
kataegis/	Regional hypermutation events (4+ SNVs)
other/	Clustered events with inconsistent allele frequencies (only present when VAF/CCF data is available)

When probability=True, an extra column is appended to each VCF file containing the probability of observing that clustered event within its local genomic region.

nonClustered/ Directory

Contains VCF files with the non-clustered mutations for each sample. Substitution and indel mutations are stored in separate files, one per sample.

plots/ Directory

Contains two types of visualizations generated per sample:

IMD plots

Show the mutational spectra alongside the distribution of inter-mutational distances (IMD) for both the real data and the simulated background. These plots allow visual inspection of the clustering signal relative to the background model.

Rainfall plots

Display the IMD distribution across genomic coordinates for each sample, with the sample-dependent IMD threshold overlaid. Clustered events are color-coded by subclass, providing a genome-wide view of mutational clustering patterns.

simulations/ Directory

Contains three subdirectories with intermediate simulation data used for threshold calculation:

Subdirectory	Contents
imd_data/	IMD values across all simulations
original_imds/	IMD values for the original (real) mutations
sorted_sims/	Simulation files sorted alphanumerically, used during threshold computation

vcf_files_corrected/ Directory

Contains VCF files for both clustered and non-clustered mutations after the localized IMD correction step (Stage 3 of the workflow). These files reflect the final mutation assignments incorporating regional mutation density adjustments.

Mutation Class Summary

Output files use the following class labels to describe the nature of each clustered event:

Class	Categories included	Description
Class 1	DBS, MBS, Omikli	Small-scale clustered events involving 2–3 mutations
Class 2	Kataegis	Larger hypermutation events; further subdivided by processivity
Class 3	Other clustered	Remaining clustered mutations not fitting Class 1 or Class 2 criteria

Each output VCF row includes the mutation coordinates, alleles, IMD value, and allele frequency, enabling detailed downstream analysis of individual clustered events.