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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

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

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)

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

Enabling vcf_files Output

To generate vcf_files output, set seqInfo=True:

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