From raw VCF to prioritized findings, VarSeq delivers an integrated variant analysis workflow with real-time filter chains, curated annotation sources, and phenotype-driven prioritization across panels, exomes, and genomes.
VarSeq combines curated annotation, real-time filter chains, and phenotype-driven prioritization into a single platform. No scripting required, whether you're analyzing gene panels or whole genomes.
Automatically annotate variants at import with ClinVar, gnomAD, OMIM, LOVD, CADD, and more. Monthly curated updates keep your knowledge current without external dependencies.
Build real-time filter chains with complex nested logic (AND, OR, NOT) combining population frequency, inheritance patterns, functional impact, and quality metrics. Rapidly refine results without rerunning pipelines.
Rank variants by phenotype relevance using HPO and OMIM biomedical ontologies. The PhoRank algorithm surfaces the most phenotypically relevant candidates, reducing review time for exomes and genomes.
VarSeq's end-to-end pipeline connects every step of variant analysis into a single reproducible, auditable workflow.
Import VCF files and automatically annotate against curated databases: ClinVar, gnomAD, OMIM, LOVD, and functional predictors like SIFT and PolyPhen2.
Apply real-time filter chains with nested logic: population frequency, inheritance mode (de novo, compound het, X-linked), functional impact, and phenotype-driven PhoRank scoring.
Verify candidates in Golden Helix GenomeBrowse with BAM pileup, coverage tracks, ClinVar overlays, and transcript context. Inspect read-level evidence to confirm variant calls.
Evaluate variants in VSClinical with automated ACMG criteria scoring, probabilistic pathogenicity assessment, and integrated evidence from population data and functional predictions.
Generate structured assessment reports integrating variants, classifications, evidence, and quality metrics. Archive results in VSWarehouse for longitudinal tracking and reanalysis.
Consistent, reproducible annotation is the foundation of clinical variant analysis. VarSeq stores all annotation data locally and updates it monthly, so your results never depend on external service availability.
Request a personalized demo of the variant analysis workflow.
VarSeq's real-time filter chain engine supports every analysis scenario with full nested logic (AND, OR, NOT). Analyze family-based inheritance, cohort comparisons, and rapid iterative exploration across all imported and annotated data.
Full pedigree support: de novo, autosomal dominant and recessive, X-linked, compound heterozygous, and custom sample groupings for cohort analysis.
gnomAD, 1000 Genomes with configurable AF thresholds and sub-population filtering.
De novo, autosomal dominant/recessive, X-linked, compound het. Full pedigree with trio/quad support.
Loss-of-function prioritization, missense constraint, splice-site impact, and sequence ontology terms.
HPO-driven PhoRank scoring, coverage quality thresholds, and regional BED file analysis.
The annotation, filter chains, and prioritization described above are part of both VarSeq Suite (licensed for Research Use Only) and VarSeq Dx (an in vitro diagnostic medical device CE-marked under Regulation (EU) 2017/746). Same software capabilities, different regulatory configurations.
Load trio data, apply inheritance filters (de novo, compound het), and use PhoRank phenotype-driven ranking to shorten the diagnostic odyssey across exomes and genomes.
Annotate and filter hundreds of thousands of variants to a manageable review set. Combine population frequency, functional impact, and gene-disease overlays to surface prioritized findings fast.
Detect low-frequency somatic mutations with allelic ratio filtering, annotate against COSMIC and known cancer hotspots, and apply the Cancer Classifier for automated variant prioritization in tumor samples.
Deep dives into variant filtering strategies, annotation best practices, and clinical analysis workflows.
Join leading clinical laboratories worldwide using VarSeq for integrated variant filtering, annotation, and interpretation.