cyanea/vcf-explorer
WASMExplore VCF files with filtering, sorting, and annotation lookups. Supports multi-sample VCFs with genotype visualization.
Overview
VCF Explorer lets you load, filter, and browse variant call files entirely in the browser. Supports single-sample and multi-sample VCFs with interactive genotype matrices, quality filtering, and region-based queries — no server or installation needed.
Features
- Interactive table — Sort by position, quality, allele frequency, or any INFO/FORMAT field.
- Smart filtering — Filter by quality (QUAL), read depth (DP), allele frequency (AF), variant type (SNP/indel/SV), and custom expressions.
- Genotype matrix — Multi-sample VCFs rendered as a color-coded genotype grid (ref/het/hom-alt/missing).
- Region queries — Zoom into a chromosome region or search by rsID.
- Summary statistics — Ts/Tv ratio, variant density per chromosome, allele frequency spectrum.
- Export — Download filtered variants as a new VCF or TSV for downstream analysis.
How It Works
The tool uses cyanea-io compiled to WASM for fast VCF parsing, including gzipped files. Filtering and aggregation use cyanea-stats for statistical summaries. All processing happens in a Web Worker so the UI stays responsive even with millions of variants.
Use Cases
- Variant triage — Quickly filter a clinical VCF to candidate pathogenic variants.
- QC review — Check Ts/Tv ratios and depth distributions before joint calling.
- Teaching — Explore population VCFs (e.g., 1000 Genomes subsets) interactively.
- Cohort overview — Visualize genotype patterns across dozens of samples.