cohort¶

Aggregate outputs from multiple pipeline runs into a single cohort summary.

Synopsis¶

vntyper [global-options] cohort
    (-i <dir> [<dir> ...] | --input-file <file>)
    -o <dir>
    [--summary-file <name>]
    [--summary-formats <formats>]
    [--pseudonymize-samples [<basename>]]

Arguments¶

Option	Type	Default	Description
`-i, --input-dirs`	list	—	List of directories containing output files to aggregate. Mutually exclusive with `--input-file`
`--input-file`	path	—	Path to a newline-separated text file listing directories or zip files to aggregate. Mutually exclusive with `-i`
`-o, --output-dir`	path	(required)	Output directory for the aggregated summary
`--summary-file`	string	`cohort_summary.html`	Name of the cohort summary report file
`--summary-formats`	string	`""`	Comma-separated list of additional summary output formats to generate (supported: `csv`, `tsv`, `json`). HTML is always generated
`--pseudonymize-samples`	string (optional value)	—	Pseudonymize sample names to protect sensitive information. When used without a value, defaults to the basename `sample_`. Optionally provide a custom basename

One of -i/--input-dirs or --input-file is required.

Pseudonymization¶

The --pseudonymize-samples flag supports two modes:

Default basename: --pseudonymize-samples (no value) uses sample_ as the prefix, producing names like sample_a3f8c, sample_1b2d0 (prefix + first 5 characters of the MD5 hash of the original sample name).
Custom basename: --pseudonymize-samples patient_ uses the provided prefix, producing names like patient_a3f8c, patient_1b2d0.

Examples¶

Aggregate results from multiple directories:

vntyper cohort -i results/sample1/ results/sample2/ results/sample3/ -o cohort_output/

Aggregate from a file listing directories:

vntyper cohort --input-file sample_dirs.txt -o cohort_output/

Generate additional output formats with pseudonymized sample names:

vntyper cohort -i results/*/ -o cohort_output/ \
    --summary-formats csv,tsv,json --pseudonymize-samples

Use a custom pseudonymization prefix:

vntyper cohort -i results/*/ -o cohort_output/ --pseudonymize-samples patient_