AlignVCF
VCF annotation, filtering, and clinical variant analysis
The Challenge
Variant calling pipelines produce VCF files containing thousands to millions of variants, but the raw output is far from actionable. Researchers need to annotate variants with clinical significance, population frequencies, and functional impact — then filter down to the variants that matter for their specific research question.
Navigating databases like ClinVar, gnomAD, and Ensembl VEP requires specialized knowledge, and integrating annotations from multiple sources into a coherent analysis workflow is technically demanding. Without proper filtering and quality assessment, important variants get buried in noise.
How AlignVCF Helps
AlignVCF provides a complete VCF annotation and analysis pipeline through a dark-themed Shiny interface optimized for extended analysis sessions. Upload your VCF file and receive comprehensive annotations from ClinVar (clinical significance), gnomAD (population allele frequencies), and VEP (functional impact predictions).
The interactive filtering system lets you narrow variants by clinical significance, population frequency thresholds, functional consequence, and quality metrics. Filters combine dynamically, and results update in real-time so you can iteratively refine your variant set.
Quality metrics visualization provides at-a-glance assessment of your variant calls: depth distribution, quality score distributions, transition/transversion ratios, and per-sample statistics. These metrics help identify potential quality issues before downstream analysis.
Results can be exported as annotated TSV files, filtered VCF files, or comprehensive PDF reports suitable for clinical research documentation.
What You Receive
Annotated Variant Table
Every variant annotated with ClinVar clinical significance, gnomAD population frequencies, VEP functional predictions, and gene-level information.
Filtered Variant Sets
Curated variant lists filtered by your criteria — pathogenic/likely pathogenic variants, rare variants, coding variants, or custom filter combinations.
Quality Assessment
Comprehensive quality metrics report with visualizations of depth, quality scores, variant type distributions, and per-sample statistics.
Export Package
Annotated TSV files, filtered VCF files, and PDF summary reports ready for clinical research documentation or downstream analysis.
Methodology
gnomAD
VEP
VariantAnnotation
Bioconductor
AlignVCF uses the Bioconductor VariantAnnotation package for VCF parsing and annotation. Clinical significance is sourced from NCBI ClinVar (updated monthly), population frequencies from gnomAD v4, and functional impact predictions from Ensembl VEP.
Variant classification follows ACMG/AMP guidelines where applicable. Quality filtering thresholds are based on GATK best practices recommendations. All annotation databases are versioned for reproducibility.
Ideal For
- Clinical research studies requiring variant annotation with ClinVar pathogenicity classifications
- Rare disease research filtering for candidate pathogenic variants
- Cancer genomics projects annotating somatic mutations with functional impact
- Population genetics studies requiring allele frequency filtering
- Any project with VCF files that need systematic annotation and quality assessment
Start Your Analysis
Ready to analyze your data with AlignVCF? Submit your project and we'll scope a plan tailored to your experimental design.