Quick Start¶

Run your first VNtyper 2 analysis in 5 minutes.

1. Install VNtyper 2¶

Follow the Installation guide to install VNtyper 2 and its dependencies.

2. Download Reference Files¶

VNtyper 2 needs reference sequences and motif databases before it can run. Download them to a local directory:

vntyper install-references -d ./references

This downloads chromosome 1 references (hg19/hg38) and MUC1 motif databases, then builds BWA indices. See Reference Setup for details.

3. Run the Pipeline¶

Analyze a BAM file with the default Kestrel genotyping engine:

vntyper pipeline \
    --bam sample.bam \
    -o results/ \
    --threads 4 \
    --reference-assembly hg38

Don't have a BAM file?

Download the VNtyper 2 test dataset (~1.1 GB) to try it out:

make download-test-data

Then run the pipeline on the test BAM file located in the test data directory.

For paired-end FASTQ input:

vntyper pipeline \
    --fastq1 sample_R1.fastq.gz \
    --fastq2 sample_R2.fastq.gz \
    -o results/ \
    --threads 4

Add --fast-mode to skip filtering for unmapped and partially mapped reads, speeding up the analysis.

4. View Results¶

Once the pipeline completes, the output directory contains:

results/
  pipeline.log                  # Full pipeline log
  pipeline_summary.json         # Machine-readable summary
  kestrel/
    kestrel_result.tsv          # Genotyping results (main output)
    output_indel.vcf            # Filtered INDEL VCF
    output.bam                  # Kestrel alignments
  fastq_bam_processing/         # Extracted FASTQ reads
  alignment_processing/         # BWA-aligned BAM (FASTQ input)
  coverage/                     # Coverage statistics

The primary output is kestrel/kestrel_result.tsv, which contains detected MUC1 VNTR variants with confidence scores, frameshift analysis, and depth metrics.

5. Generate an HTML Report¶

Create a visual summary report with IGV integration:

vntyper report \
    -o results/ \
    --input-dir results/

Open the generated HTML file in your browser to review:

VNTR region coverage statistics
Genotyping calls from Kestrel
Quality metrics (duplication rate, Q20/Q30 rates)
Pipeline execution log

What's Next?¶

Reference Setup --- Configure references for different genome assemblies
User Guide --- Explore advanced pipeline options, optional modules (adVNTR, SHARK), and Docker usage