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Running the Pipeline

Minimal Run

vntyper pipeline --bam sample.bam -o results/

This uses default settings: hg19 assembly, 4 threads, Kestrel genotyping only.

Common Options

vntyper pipeline --bam sample.bam -o results/ \
    --threads 8 \
    --fast-mode \
    --reference-assembly hg38
Option Effect
--threads N Number of threads (default: 4)
--fast-mode Skip filtering for unmapped and partially mapped reads (faster)
--reference-assembly Assembly used for alignment (default: hg19). See Reference Assemblies
--sample-name Label for results. Defaults to input filename stem
--output-name Base name for intermediate output files (default: processed)

With adVNTR Module

vntyper pipeline --bam sample.bam -o results/ \
    --extra-modules advntr

adVNTR provides independent VNTR genotyping. Results are cross-matched with Kestrel calls. Use --advntr-max-coverage 300 for faster adVNTR runs on high-coverage samples.

With SHARK Module (FASTQ Only)

vntyper pipeline --fastq1 R1.fastq.gz --fastq2 R2.fastq.gz -o results/ \
    --extra-modules shark

Warning

SHARK only works with FASTQ input. Using --extra-modules shark with --bam or --cram will cause an error.

Custom Regions

Override the default MUC1 VNTR region coordinates:

vntyper pipeline --bam sample.bam -o results/ \
    --custom-regions chr1:155160500-155162000

Multiple regions are comma-separated: chr1:1000-2000,chr1:3000-4000

vntyper pipeline --bam sample.bam -o results/ \
    --bed-file regions.bed

--custom-regions and --bed-file are mutually exclusive.

Archiving Results

vntyper pipeline --bam sample.bam -o results/ \
    --archive-results --archive-format tar.gz

Creates a compressed archive of the output directory after the pipeline completes. Supported formats: zip (default) and tar.gz.

Additional Summary Formats

vntyper pipeline --bam sample.bam -o results/ \
    --summary-formats csv,tsv

Generates pipeline_summary.csv and/or pipeline_summary.tsv alongside the default JSON summary.

Intermediate Files

Option Effect
--keep-intermediates Retain BAM slices, temporary FASTQ files, etc.
--delete-intermediates Delete intermediate files after processing (overrides --keep-intermediates)

Custom Configuration

vntyper --config-path /path/to/custom/config.json pipeline --bam sample.bam -o results/

Note that --config-path is a global option and must appear before the subcommand. See Configuration for details.

Logging

vntyper -l DEBUG pipeline --bam sample.bam -o results/

Log levels: DEBUG, INFO (default), WARNING, ERROR, CRITICAL. The pipeline log is automatically written to <output-dir>/pipeline.log. Override with -f /path/to/logfile.