Online Mode¶

The online subcommand submits a BAM file to vntyper.org for cloud-based analysis. VNtyper 2 automatically subsets your BAM to the MUC1 region before uploading, so only a small file is transferred.

Basic Usage¶

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

This will:

Extract the MUC1 region from your BAM using samtools
Upload the subset BAM to the vntyper.org API
Poll for job completion
Download results to the output directory

Email Notifications¶

Receive an email when your job completes:

vntyper online --bam sample.bam -o results/ \
    --email user@example.com

Cohort Submission¶

Associate your submission with a cohort on vntyper.org:

vntyper online --bam sample.bam -o results/ \
    --cohort-id my_study_2024 \
    --passphrase secret123

Resume Polling¶

If the CLI is interrupted during polling, resume without re-uploading:

vntyper online --bam sample.bam -o results/ --resume

This reads the saved job_id.txt from the output directory and resumes status polling.

Options Reference¶

Option	Description
`--bam`	Path to input BAM file (required)
`-o`, `--output-dir`	Output directory for results (default: `out`)
`--reference-assembly`	Assembly used for alignment (default: hg19)
`--threads`	Number of threads for BAM subsetting (default: 4)
`--email`	Email for job completion notification
`--cohort-id`	Cohort ID to associate the job with
`--passphrase`	Passphrase for cohort access
`--resume`	Resume polling a previously submitted job

Note

The online mode API endpoint is configured in config.json under api.base_url (default: https://vntyper.org/api).