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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.

Tool

bash + bcftools (for extracting counts from VCF files)

Docker Image

staphb/bcftools:1.21 (already used by other steps)

Input

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