report¶

Generate an HTML summary report and visualizations from pipeline output data.

Synopsis¶

vntyper [global-options] report
    -o <dir>
    [--input-dir <dir>]
    [--report-file <name>]
    [--bed-file <file>] [--bam-file <file>] [--reference-fasta <file>]
    [--flanking <int>]

Arguments¶

Option	Type	Default	Description
`-o, --output-dir`	path	(required)	Directory containing pipeline results
`--input-dir`	path	—	If provided, search this directory (and its subdirectories) for standard pipeline output filenames
`--report-file`	string	`summary_report.html`	Name of the output report file
`--bed-file`	path	—	Path to the BED file for IGV reports
`--bam-file`	path	—	Path to the BAM file for IGV reports
`--reference-fasta`	path	(from config)	Path to the reference FASTA file for IGV reports. Falls back to `muc1_reference_vntr` in config if not provided
`--flanking`	int	`50`	Flanking region size for IGV reports

Auto-Discovery¶

When --input-dir is provided and --bam-file or --bed-file are not specified, the report command will attempt to auto-discover standard pipeline output files:

BAM file: <input-dir>/kestrel/output.bam
BED file: <input-dir>/kestrel/output.bed

Examples¶

Generate a report from pipeline output:

vntyper report -o results/ --input-dir results/

Generate a report with custom IGV settings:

vntyper report -o results/ \
    --bam-file results/kestrel/output.bam \
    --bed-file results/kestrel/output.bed \
    --reference-fasta ref/muc1.fa \
    --flanking 100

Generate a report with a custom filename:

vntyper report -o results/ --input-dir results/ --report-file my_report.html