Using SigProfilerSimulator - Output¶

This section describes the output files and directories produced by SigProfilerSimulator. All results are written under the project directory specified in project_path.

Output Overview¶

After a successful run, the project directory contains the following structure:

[project_path]/
├── input/
│   └── [input mutation files]
├── output/
│   └── simulations/
│       └── [project]_simulations_[genome]_[contexts]/
│           ├── 1.maf
│           ├── 2.maf
│           └── ...
└── logs/
    ├── SigProfilerSimulator_[project]_[genome]_[date].err
    └── SigProfilerSimulator_[project]_[genome]_[date].out

The output subdirectory name includes a suffix depending on the simulation scope:

Condition	Output subdirectory suffix
Whole genome (default)	`[project]_simulations_[genome]_[contexts]/`
BED file restricted (`bed_file`)	`[project]_simulations_[genome]_[contexts]_BED/`
Exome restricted (`exome=True`)	`[project]_simulations_[genome]_[contexts]_exome/`

Simulation Files¶

MAF format (default)¶

When vcf=False (default), one MAF file is produced per simulation, named 1.maf, 2.maf, etc. Each file contains all samples for that simulation iteration.

MAF files contain the following 17 columns:

Column	Description
`Hugo_symbol`	Gene symbol
`Entrez_gene_ID`	Entrez gene identifier
`Center`	Sequencing center
`Genome`	Reference genome used
`Chrom`	Chromosome
`Start_position`	Mutation start position (1-based)
`End_position`	Mutation end position (1-based)
`Strand`	Genomic strand
`Variant_Classification`	Mutation functional class
`Variant_Type`	Mutation type (SNP, INS, DEL)
`Reference_Allele`	Reference base(s)
`Tumor_Seq_Allele1`	First tumor allele
`Tumor_Seq_Allele2`	Second tumor allele
`dbSNP_RS`	dbSNP RS identifier
`dbSNP_Val_Status`	dbSNP validation status
`Tumor_Sample_Barcode`	Sample identifier
`matGenClass`	Mutational context classification

VCF format¶

When vcf=True, a separate subdirectory is created per sample within the output folder. Each subdirectory contains one VCF file per simulation:

[project]_simulations_[genome]_[contexts]/
├── [sample_1]/
│   ├── [sample_1]_1.vcf
│   ├── [sample_1]_2.vcf
│   └── ...
└── [sample_2]/
    ├── [sample_2]_1.vcf
    └── ...

Log Files¶

Two log files are saved per run in the logs/ subdirectory:

File	Description
`SigProfilerSimulator_[project]_[genome]_[date].out`	Progress checkpoints and run parameters
`SigProfilerSimulator_[project]_[genome]_[date].err`	Error messages and warnings

Sequence Context Files¶

When seqInfo=True, additional files containing the sequence context of each simulated mutation are saved under:

[project_path]/output/vcf_files/simulations/[context]/

One file is saved per sample, chromosome, and simulation: [sample]_[chrom]_seqinfo_[n].txt.