User Guide¶

This section covers running VNtyper 2 and interpreting its outputs:

• Input Formats: Supported BAM, CRAM, and FASTQ input requirements.
• Running the Pipeline: Command examples from minimal to advanced usage.
• Output Files: Directory structure, result columns, and confidence levels.
• Configuration: Customizing config.json and kestrel_config.json.
• Reference Assemblies: Supported assemblies, naming conventions, and auto-detection.
• Docker: Running VNtyper 2 in Docker and Apptainer containers.
• Cohort Analysis: Aggregating results across multiple samples.
• Online Mode: Submitting jobs to vntyper.org from the CLI.