Step 24: HTML Report
What This Does
Generates a self-contained HTML dashboard summarizing all pipeline results. Open it in any browser — no internet connection needed.
Why
The pipeline produces output across many directories in different formats (VCF, TSV, HTML, TXT). This step consolidates everything into a single visual report with color-coded status indicators, variant counts, and key findings.
bash + bcftools (for extracting counts from VCF files)
Docker Image
staphb/bcftools:1.21 (already used by other steps)
All output directories from previous pipeline steps. The script automatically detects which steps have been run.
Command
./scripts/24-html-report.sh your_name
Output
A single file: ${GENOME_DIR}/${SAMPLE}/${SAMPLE}_report.html
Typically 10-30 KB. Contains:
- Variant Calling — total variants, PASS count, SNPs, indels
- ClinVar Screening — hit count with top 20 detailed in a table
- Pharmacogenomics — PharmCAT report status
- Structural Variants — Manta, Delly, CNVnator counts
- Cancer Predisposition — CPSR report status
- Repeat Expansions — key loci repeat counts (HTT, FMR1, C9orf72, etc.)
- Ancestry & Identity — haplogroup, ROH, telomere content
- Mitochondrial — chrM variant and heteroplasmy counts
- Clinical Filter — interesting variant counts from step 23
Runtime
1-3 minutes (mostly Docker startup time for bcftools queries)
How to Open
# macOS
open ${GENOME_DIR}/${SAMPLE}/${SAMPLE}_report.html
# Linux
xdg-open ${GENOME_DIR}/${SAMPLE}/${SAMPLE}_report.html
# Windows (WSL)
start ${GENOME_DIR}/${SAMPLE}/${SAMPLE}_report.html
Notes
- The report is completely self-contained — all CSS is inline, no external dependencies
- Works offline in any modern browser
- Responsive layout (works on mobile/tablet)
- Steps that were not run show “N/A” or “Not run” — this is expected
- The report does NOT contain any variant-level data beyond the ClinVar hits table — it is safe to share without exposing raw genomic data
- Re-run this script anytime to update the report after running additional steps