User Guide¶

This section covers everything you need to run VNtyper 2 and interpret its results.

• 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.
• Snakemake -- Batch processing with Snakemake workflows.