pipeline¶

Run the full VNtyper 2 genotyping pipeline.

Synopsis¶

vntyper [global-options] pipeline
    (--bam <file> | --cram <file> | --fastq1 <file> --fastq2 <file>)
    [-o <dir>] [-n <name>] [-s <name>]
    [--reference-assembly <assembly>] [--custom-regions <regions> | --bed-file <file>]
    [--threads <int>] [--fast-mode] [--keep-intermediates] [--delete-intermediates]
    [--extra-modules <module> ...]
    [--advntr-max-coverage <int>]
    [--archive-results] [--archive-format <format>]
    [--summary-formats <formats>]

Input Options¶

Provide exactly one input type: BAM, CRAM, or paired FASTQ files.

Option	Type	Default	Description
`--bam`	path	—	Path to the BAM file
`--cram`	path	—	Path to the CRAM file
`--fastq1`	path	—	Path to the first FASTQ file (paired-end)
`--fastq2`	path	—	Path to the second FASTQ file (paired-end)

When using FASTQ input, both --fastq1 and --fastq2 are required.

Output Options¶

Option	Type	Default	Description
`-o, --output-dir`	path	`out`	Output directory for the results
`-n, --output-name`	string	`processed`	Base name for the output files
`-s, --sample-name`	string	(from input filename)	Sample name for labeling results. If not provided, defaults to the input BAM or FASTQ filename stem

Reference & Region Options¶

Option	Type	Default	Description
`--reference-assembly`	choice	`hg19`	Reference assembly for BAM/CRAM alignment. Options: `hg19`, `hg38`, `GRCh37`, `GRCh38`, `hg19_ncbi`, `hg38_ncbi`, `hg19_ensembl`, `hg38_ensembl`
`--custom-regions`	string	—	Custom regions for MUC1 analysis as comma-separated values (e.g., `chr1:1000-2000,chr2:3000-4000`)
`--bed-file`	path	—	Path to a BED file specifying regions for MUC1 analysis

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

Processing Options¶

Option	Type	Default	Description
`--threads`	int	`4`	Number of threads to use
`--fast-mode`	flag	off	Enable fast mode (skips filtering for unmapped and partially mapped reads)
`--keep-intermediates`	flag	off	Keep intermediate files (e.g., BAM slices, temporary files)
`--delete-intermediates`	flag	off	Delete intermediate files after processing. Overrides `--keep-intermediates`

Optional Modules¶

Option	Type	Default	Description
`--extra-modules`	string	`[]`	Optional extra modules to include (e.g., `advntr`, `shark`). Can be repeated multiple times
`--advntr-max-coverage`	int	—	Max coverage (e.g., 300) for quick adVNTR mode. Only applies when `advntr` is in `--extra-modules`

The shark module is not supported in BAM/CRAM mode; use FASTQ mode or remove the shark flag.

Archive & Summary Options¶

Option	Type	Default	Description
`--archive-results`	flag	off	Create an archive of the results folder after pipeline completion
`--archive-format`	choice	`zip`	Format of the archive: `zip` or `tar.gz`
`--summary-formats`	string	`""`	Comma-separated list of additional summary output formats to generate (supported: `csv`, `tsv`). JSON is always generated

Examples¶

Run the pipeline with a BAM file using default settings:

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

Run with paired FASTQ files and hg38 reference:

vntyper pipeline --fastq1 R1.fastq.gz --fastq2 R2.fastq.gz \
    --reference-assembly hg38 -o results/ -s my_sample

Enable fast mode with multiple threads and archive results:

vntyper pipeline --bam sample.bam -o results/ --threads 8 \
    --fast-mode --archive-results --archive-format tar.gz

Run with the adVNTR module and coverage cap:

vntyper pipeline --bam sample.bam -o results/ \
    --extra-modules advntr --advntr-max-coverage 300

Generate additional summary formats and clean up intermediate files:

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