Whole exome analysis
Whole exome bioinformatics & analysis
Expert-led secondary analysis delivering high-fidelity variant detection and deep functional annotation — GATK gold-standard workflows and multi-caller consensus filtering, managed directly by the computational team.
GATK
gold-standard best practices
0 callers
Mutect2, Strelka2 & VarDict consensus
hg19 / hg38
reference assemblies supported
AWS
scalable encrypted cloud
Scalable bioinformatics solutions
Tiered computational workflows
From high-volume population cohorts to rare somatic mutations — tiered analysis models turn exome data into high-confidence, publication-ready insight.
Standard Analysis
Rapid, automated analysis for high-volume genomic research.
- Data QC report + raw FASTQ
- Alignment (BAM) file
- Germline VCF + germline variant annotation
- Low-frequency germline variant calling & annotation
Best for high-throughput germline screening and standard cohort studies.
Request this serviceAdvanced Analysis
Deep-dive genomic profiling for complex mutational landscapes. Includes everything in Standard, plus:
- Somatic mutation annotation
- Low-frequency somatic variant calling & annotation
- Joint genotyping
- Structural variant calling
- Tumor/normal CNV calling
- gVCF output
Best for tumor-normal studies, somatic driver discovery and translational research.
Request this serviceCustomized Analysis
Tailored bioinformatics outputs built for your specific project.
- Everything in Advanced
- Custom analysis based on project requirements
- Defined depth and allele-frequency cutoffs
- Database-specific annotations (COSMIC, gnomAD)
Best for specialized study designs and custom filtering strategies.
Request this serviceFTE BioFx Team
Dedicated computational experts for long-term analysis needs.
- An embedded bioinformatician on your program
- Iterative data mining and reanalysis
- Custom pipeline and tool development
Best for pharma and biotech teams with sustained analysis volume.
Request this serviceThe Gateway advantage
Computational precision & transparency
GATK gold-standard pipelines
Industry-validated GATK Best Practices for alignment and variant calling — the highest bar for sensitivity and reproducibility.
Multi-tool consensus calling
Mutect2, Strelka2 and VarDict consensus minimizes false positives for the most robust SNV and indel sets.
Deep functional annotation
Every variant enriched with ClinVar, gnomAD and COSMIC context to prioritize high-impact mutations fast.
End-to-end transparency
No black box — all primary and secondary data including FASTQ, aligned BAM and filtered VCF for complete auditability.
Scalable cloud architecture
Secure AWS-powered infrastructure processes hundreds of exomes simultaneously without compromising depth.
Scientist-to-scientist support
Skip the ticketing system — work directly with the bioinformatics team on filtering parameters or custom workflows.
Processing workflow
From raw reads to actionable results
Step 1
Consultation
Define analysis goals — from germline screening to somatic driver identification.
Step 2
Data ingestion
Upload FASTQ from any Illumina platform via encrypted SFTP or AWS S3 transfer.
Step 3
Processing & QC
Validated pipelines with rigorous per-sample and per-batch quality metrics.
Step 4
Variant prioritization
Expert-led functional annotation and filtering to isolate high-interest variants.
Step 5
Delivery & reporting
Complete data package with publication-ready visualizations and comprehensive PDF summaries.
Beyond the FASTQ
Outputs we deliver
All analysis outputs based on the package chosen — BAM, VCF and more — plus a publication-ready report.
Deliverables include
SNV & indel distribution
Somatic variant analysis
CNV & structural events
Publication-ready figures
SNV & indel distribution
Somatic variant analysis
CNV & structural events
Publication-ready figures
Aligned BAM files
Germline & somatic VCF
Joint genotyping & gVCF
Tumor mutational burden (TMB)
Aligned BAM files
Germline & somatic VCF
Joint genotyping & gVCF
Tumor mutational burden (TMB)
Figures & files delivered with every project — hover to pause
Applications
Where this service delivers
Oncology & tumor profiling
Detect somatic variants and driver mutations.
Pharmacogenomics
Understand how genetic variation impacts drug response.
Population genetics
Large-scale cohort studies for genomic discovery.
Germline & somatic detection
Identify inherited and acquired genetic variations.
Targeted discovery
Focus on protein-coding regions where most disease-associated variants occur.
Rare disease research
Identify causative mutations in complex phenotypes.
FAQs
Plan your project
Resources & insights
Go deeper
Explore related sequencing solutions
Sequencing & analysis services
Start your exome analysis
Tell us about your data and research goals — a PhD scientist replies within one business day with the right analysis workflow and a tailored quote.
- Auditable, expert-led bioinformatics
- GATK + multi-caller consensus
- WES analysis, annotation & interpretation
Ready to launch your study?
Share your samples and goals — a doctoral-level scientist responds within one business day with a study plan and competing blind quotes.
- Expert-guided study design & service matching
- Competitive quotes, adaptable turnaround times
- End-to-end bioinformatics & reporting
- Run by accredited facilities across the nationwide network
Administered by Syntax of Life Private Limited
Request a quote