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.
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.