Wong M, Liew B, Hum M, Lee NY, Lee ASG. Benchmarking of variant calling software for whole-exome sequencing using gold standard datasets. Sci Rep. 2025;15(1):13697. doi:10.1038/s41598-025-97047-7
A recent benchmarking study in Scientific Reports1 compares no-code platforms for whole-exome sequencing (WES) variant calling and interpretation. The independent evaluation compared four leading solutions: Illumina BaseSpace Sequence Hub, CLC Genomics Workbench, Partek Flow, and VarSome Clinical. We’re proud to see VarSome Clinical recognised for its strengths in clinical annotation, ease of use, and supporting precision medicine initiatives.
Meeting the Growing Need for Accessible Genomics
Variant calling is a critical step in genomic analysis, but traditional workflows often require specialist bioinformatic skills. As the global demand for genomic medicine grows, so does the need for platforms that empower clinicians, researchers, and smaller laboratories to perform high-quality analyses without the need for programming experience.
Expanding access to genomic analysis tools is essential for advancing precision medicine globally, helping to make sure that innovations in healthcare reach a broader range of patients and settings.
Key Findings
Illumina’s DRAGEN Enrichment pipeline produced the most accurate secondary calls in the benchmark. Across three GIAB WES reference datasets, its mean F1 scores for SNVs and indels were 99.69% and 96.99%, respectively.
VarSome Clinical’s Sentieon-powered caller followed closely. Wong et al. report a cluster mean SNV F1 over 98%, and indel F1 scores are between 89% and 93%. Where VarSome pulls ahead is in tertiary analysis. Its workflow layers a germline classifier based on ACMG/AMP pathogenicity rules and a cross-referenced knowledge base directly over raw calls, turning VCFs into pathogenicity assessments in a single step. DRAGEN does not offer an equivalent interpretation module, but its VCF output imports straight into VarSome Clinical.
While DRAGEN leads raw-calling accuracy, VarSome Clinical simplifies the route to a signed-off report: import DRAGEN calls for classification and annotation, or run VarSome end-to-end for an integrated, evidence-backed workflow.
Connecting Data and Decisions
VarSome Clinical brings together variant annotation, classification, and interpretation within a single platform. By consolidating these critical steps, it reduces the need for additional tools or specialist bioinformatics support, helping laboratory teams translate sequencing data into meaningful clinical insights.
This integrated approach is particularly valuable in clinical environments, where timely and accurate decision-making is essential. By supporting applications including rare disease diagnosis, family trio WES, oncology, and more, VarSome Clinical helps laboratories of all sizes deliver faster, more informed patient care.
Read the Full Study
VarSome Clinical’s strengths in clinical interpretation, accessibility, and intuitive design are helping to expand access to precision medicine. By enabling high-quality genomic analysis without the need for specialist bioinformatics expertise, it supports clinical laboratories, research centres, and institutions in low-resource settings to make effective use of modern genomic technologies.
Interested in reading the full comparison? You can find the benchmarking study here.
Have questions or want to learn more? We’d love to hear from you. You can get in touch with us at sales@varsome.com or by filling in our contact form. Alternatively, you can visit our website to find out more.
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