Output vcf_files

Output - vcf_files

This page describes the vcf_files output folder structure.

Overview

The vcf_files folder contains text-based files with original mutations paired with their SigProfilerMatrixGenerator classifications.

Folder Structure

vcf_files/
├── DBS/     # Dinucleotide substitutions
├── MNS/     # Multinucleotide substitutions
├── SNV/     # Single nucleotide variants
└── ID/      # Small insertions and deletions

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Subfolders

DBS (Dinucleotide Substitutions)

Contains files with double base substitution mutations and their DBS classifications.

Output includes:

• Original mutation coordinates
• Reference dinucleotide
• Alternate dinucleotide
• DBS classification category

MNS (Multinucleotide Substitutions)

Contains mutations involving 3 or more consecutive nucleotides.

Output includes:

• Mutation coordinates
• Reference sequence
• Alternate sequence
• MNS classification

SNV (Single Nucleotide Variants)

Contains single base substitutions with their SBS classifications.

Output includes:

• Chromosome and position
• Reference nucleotide
• Alternate nucleotide
• Sequence context
• SBS96 classification
• Transcriptional strand information

ID (Insertions and Deletions)

Contains small insertions and deletions with their ID classifications.

Output includes:

• Mutation coordinates
• Indel sequence
• Repeat/microhomology context
• ID classification category

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File Format

Each file is tab-delimited with the following general columns:

Column	Description
Sample	Sample name
Chromosome	Chromosome identifier
Position	Genomic position
Ref	Reference allele
Alt	Alternate allele
Context	Sequence context
Classification	SigProfilerMatrixGenerator category
Strand	Transcriptional strand (if applicable)

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Usage

These files are useful for:

1. Quality control: Verify mutation classifications
2. Custom analysis: Export mutations with classifications for downstream analysis
3. Visualization: Create custom plots with mutation-level data
4. Integration: Combine with other genomic annotations

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Enabling vcf_files Output

To generate vcf_files output, set seqInfo=True:

matrices = matGen.SigProfilerMatrixGeneratorFunc(
    "project",
    "GRCh37",
    "/path/to/input",
    seqInfo=True
)