online¶

Subset a BAM file and submit it to an online VNtyper 2 instance (vntyper.org) for analysis, then poll for completion and download results.

Synopsis¶

vntyper [global-options] online
    --bam <file>
    [-o <dir>]
    [--reference-assembly <assembly>]
    [--threads <int>]
    [--email <address>]
    [--cohort-id <id>] [--passphrase <string>]
    [--resume]

Arguments¶

Option	Type	Default	Description
`--bam`	path	(required)	Path to the input BAM file
`-o, --output-dir`	path	`out`	Output directory for results
`--reference-assembly`	choice	`hg19`	Reference assembly used for alignment. Options: `hg19`, `hg38`, `GRCh37`, `GRCh38`, `hg19_ncbi`, `hg38_ncbi`, `hg19_ensembl`, `hg38_ensembl`
`--threads`	int	`4`	Number of threads to use
`--email`	string	—	Email address to receive notifications (optional)
`--cohort-id`	string	—	Cohort ID to associate the job with (optional)
`--passphrase`	string	—	Passphrase for the cohort, if required
`--resume`	flag	off	Resume polling a previously submitted job if a `job_id` is found in the output directory

Workflow¶

The online command follows a submit-poll-download workflow:

Subset: The input BAM is subsetted to the MUC1 VNTR region based on the specified reference assembly.
Submit: The subsetted BAM is uploaded to the vntyper.org server for analysis.
Poll: The command periodically checks the server for job completion.
Download: Once complete, results are downloaded to the output directory.

Use --resume to skip submission and resume polling a previously submitted job.

Examples¶

Submit a BAM for online analysis:

vntyper online --bam sample.bam -o results/ --reference-assembly hg38

Submit with email notifications and cohort association:

vntyper online --bam sample.bam -o results/ \
    --email user@example.com --cohort-id my_cohort --passphrase secret123

Resume polling a previously submitted job:

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