snippy-ng utils report sample

Create a standalone HTML report for a single sample from a VCF, with an optional embedded alignment view.

The sample report renders an interactive variant table and, when an alignment and reference are provided, an IGV.js panel showing cropped windows around each variant. It is useful for inspecting a single Snippy-NG run, sharing per-sample results, or reviewing variants before downstream interpretation.

Example report

Here is an example sample report generated with Snippy-NG.

Quick start

Generate a VCF-only sample report:

snippy-ng utils report sample short/snippy.pass.vcf

This writes the HTML report to:

report/sample.html

If you also provide an alignment, you must provide the matching reference.

snippy-ng utils report sample sample.vcf \
  --alignment sample.cram \
  --reference ref.fa

Inputs

The only required input is a VCF file.

snippy-ng utils report sample sample.vcf

To embed an alignment viewer, provide both --alignment and --reference.

snippy-ng utils report sample sample.vcf \
  --alignment sample.bam \
  --reference ref.fa

The alignment can be BAM or CRAM. Snippy-NG extracts windows around each variant and embeds the cropped alignment in the final report.

Variant selection

Use --variant-scope to choose whether the report includes only PASS variants or all variants in the input VCF.

snippy-ng utils report sample sample.vcf --variant-scope all

Use --window-size to control how many bases of context are shown around each variant when alignment windows are generated.

snippy-ng utils report sample sample.vcf --window-size 500

Output options

By default, the command writes report/sample-report.html.

Use --outdir to choose the output directory:

snippy-ng utils report sample sample.vcf --outdir results/report

Use --prefix to choose the output filename prefix:

snippy-ng utils report sample sample.vcf --outdir results/report --prefix mutant

This writes:

results/report/mutant.html

Report options

Set a custom report title:

snippy-ng utils report sample sample.vcf --title "Mutant sample report"

Override the displayed sample name:

snippy-ng utils report sample sample.vcf --sample-name mutant-01

Combine options:

snippy-ng utils report sample sample.vcf \
  --alignment sample.cram \
  --reference ref.fa \
  --variant-scope all \
  --window-size 500 \
  --title "Mutant sample report" \
  --sample-name mutant-01 \
  --outdir sample-report \
  --prefix mutant

Command reference

snippy-ng utils report sample [OPTIONS] VCF

Option	Default	Description
VCF	required	Input VCF file to render.
--alignment, --cram, --bam	none	Optional BAM or CRAM alignment to embed after windowing.
--reference, --ref	none	Reference FASTA required when --alignment is provided.
--variant-scope	pass	Include only PASS variants or all variants.
--window-size	100	Number of bases of context around each variant.
--title	Snippy-NG Sample Report	Title shown in the HTML report.
--sample-name	none	Optional sample name override.
--outdir, -o	report	Output directory.
--prefix, -p	sample	Prefix for the generated HTML file.