From whole-genome interpretation to targeted clinical panels: rigorous variant calling, annotation and reporting built on GATK Best Practices and tailored to your diagnostic, research or pharma R&D workflow.
Genomic variant analysis powers decision-making across clinical diagnostics, oncology, drug development and population research.
Identify causal variants in undiagnosed Mendelian disorders through trio analysis and ACMG-grade interpretation.
Somatic variant calling, tumor mutational burden (TMB), microsatellite instability (MSI) and actionable target identification.
Stratify patient response to medication and characterize drug-metabolizing genotypes for clinical implementation.
BRCA1/2, Lynch syndrome and broader hereditary cancer gene panel interpretation with ACMG classification.
Allele frequency comparisons, population structure analysis (PCA, ADMIXTURE) and ancestry inference.
ACMG-compliant clinical reports with PASS-filtered variants, gnomAD frequencies, ClinVar annotation and pathogenicity scores.
Full-genome variant calling and interpretation built on GATK Best Practices. From BAM/CRAM to clinically annotated, PASS-filtered VCFs with ACMG-ready reports.
GATK HaplotypeCaller in GVCF mode with joint genotyping and VQSR for cohort-aware filtering. DeepVariant available on request.
Detection of duplications, deletions and large-scale gains/losses with CNVkit, GATK gCNV or Control-FREEC.
Inversions, translocations and complex rearrangements via Manta, Delly and Lumpy with consensus calling.
GenomicsDBImport + GenotypeGVCFs for coherent multi-sample analysis. Mendelian inheritance checks for family studies.
Ensembl VEP integration with gnomAD v4, ClinVar, dbSNP, CADD, REVEL and SpliceAI for pathogenicity assessment.
Mutect2-based somatic variant calling with panel-of-normals filtering, TMB and MSI scoring for oncology workflows.
From raw FASTQ to clinically-annotated VCF, following GATK Best Practices on GRCh38 with ALT contigs.
FastQC, MultiQC and adaptive trimming on raw reads
BWA-MEM2 to GRCh38, duplicate marking and base recalibration
HaplotypeCaller in GVCF mode for joint genotyping
Gaussian mixture model trained on truth variant sets
VEP + ClinVar/gnomAD/CADD with ACMG-ready output
| Parameter | Default Specification |
|---|---|
| Reference genome | GRCh38/hg38 with ALT contigs + decoys (full GATK bundle) |
| Coverage required | ≥ 30× mean (clinical-grade); 15× minimum for research |
| Input formats | FASTQ, BAM, CRAM (full pipeline or downstream-only) |
| Variant types delivered | SNV, Indel, CNV, SV, all with PASS filters & quality scores |
| Annotation databases | VEP, gnomAD v4, ClinVar, dbSNP, CADD, REVEL, SpliceAI |
| Deliverables | Annotated VCF (bgzip + tabix), TSV table, MultiQC HTML, optional BAM |
| Typical turnaround | 2–5 business days per sample |
High-depth analysis of the protein-coding ~2% of the genome where most clinically actionable variants reside. Cost-effective alternative to WGS for diagnostic and translational research.
Capture-aware HaplotypeCaller pipeline tuned for exome enrichment kits, with hard filters and per-kit calibration.
CNV detection adapted to capture bias using CNVkit, XHMM or ExomeDepth, with batch- and kit-aware reference panels.
De novo variant calling, segregation analysis and Mendelian inheritance patterns for rare disease diagnosis.
From hereditary cancer panels to liquid biopsy with UMIs: high-depth analysis (200×–10,000×) of dozens to hundreds of clinically curated genes.
BRCA1/2, Lynch syndrome and broader hereditary cancer gene panels with ACMG classification and clinical reporting.
UMI-based error-corrected analysis for variant detection down to 0.1% allele frequency in cell-free DNA.
Longitudinal minimal residual disease tracking using patient-specific variant fingerprints for relapse prediction.
Bioinformatic design of capture panels, target region optimization and analytical validation prior to clinical deployment.
CPIC- and PharmGKB-curated variant interpretation with CYP, TPMT, DPYD and other clinically actionable drug-response genes.
Scheduled re-analysis of past samples against updated databases (ClinVar, gnomAD), flagging newly clinically relevant variants.
With VCF Visualizer Pro, our clients can safely filter variants, review clinical annotations, and analyze quality metrics directly from their browser, without the need for additional bioinformatics software.
Variant calling looks deceptively simple. But the difference between a generic VCF and a clinically defensible analysis lives in the parameter choices, the filtering strategy, and the depth of interpretation. We build pipelines that survive clinical audit, not just statistical thresholds.