Whole Exome Bioinformatics & Analysis
Accelerate your insights with Signios Bio’s expert-led secondary analysis.
We deliver high-fidelity variant detection and deep functional annotation
with industry-leading turnaround times, managed directly
by our SF Bay Area computational team.
WES Analysis: Scalable Bioinformatics Solutions
Signios Bio provides US-based computational pipelines designed for high-throughput research and complex translational studies. We bridge the gap between raw data and biological discovery by utilizing GATK Gold-Standard workflows and multi-caller consensus filtering. Whether you are analyzing high-volume population cohorts or rare somatic mutations, our tiered analysis models ensure your sequencing data is transformed into high-confidence, publication-ready insights.
Choose from our Tiered computational workflows designed for precision and scalability.
Standard Analysis
Rapid, automated analysis for high-volume genomic research.
Deliverables: FASTQ-to-VCF pipeline, GATK Best Practices (BAM), and basic annotation.
Advanced Analysis
Deep-dive genomic profiling for complex mutational landscapes.
Deliverables: Somatic mutation calling (tumor-normal) and CNV estimation.
Customized Analysis
Tailored bioinformatics outputs built for your specific project.
Deliverables: Integration of proprietary pipelines and customized data visualization.
FTE BioFx Team
Dedicated computational experts for long-term analysis needs.
Deliverables: An integrated Signios bioinformatician for your team.
SNV & Indel Distribution
Somatic Variant Analysis
CNV & Structural Events
Publication-Ready Figures
The Signios Advantage: Computational Precision & Transparency
Beyond the “Black Box”: Auditable, Expert-Led Bioinformatics.
We prioritize data integrity and transparency, providing the raw and processed files necessary for complete project auditability.
GATK Gold-Standard Pipelines
We utilize industry-validated GATK Best Practices for alignment and variant calling, ensuring your research meets the highest standards for sensitivity and reproducibility.
Multi-Tool Consensus Calling
To minimize false positives, we employ a multi-caller consensus approach (e.g., Mutect2, Strelka2, VarDict) to deliver the most robust SNV and Indel sets possible.
Deep Functional Annotation
Every variant is enriched with biological context using ClinVar, gnomAD, and COSMIC databases, allowing you to quickly prioritize high-impact mutations.
End-to-End Data Transparency
No “black box” processing. We provide all primary and secondary data—including FASTQ, aligned BAM, and filtered VCF files—for complete project auditability.
Scalable Cloud Architecture
Our secure, AWS-powered infrastructure allows us to process hundreds of exomes simultaneously, ensuring industry-leading turnaround times without compromising depth.
Scientist-to-Scientist Support
Skip the ticketing system. Work directly with our bioinformatics team to customize filtering parameters or integrate your proprietary analytical workflows.
The Signios Partnership: Analysis Processing Workflow
Step 1
Consultation
Step 2
Data Ingestion
Step 3
Processing & QC
Step 4
Variant Prioritization
Step 5
Delivery & Reporting
Define your analysis goals, from germline screening to somatic driver identification.
Upload FASTQ files from any Illumina platform via our secure, encrypted SFTP or AWS S3 transfer protocols.
Data is processed through our validated pipelines with rigorous per-sample and per-batch quality metrics.
Expert-led functional annotation and filtering to isolate variants of high biological interest.
Receive a complete data package including publication-ready visualizations and comprehensive PDF summary reports.
Resources & Insights
Service Flyer
Signios Bio’s advanced WES solutions
See how our whole-exome sequencing workflow supports different study types, from sample requirements through sequencing and data delivery..
Analysis Overview
Signios Bio bioinformatics services
End-to-end pipelines transforming raw sequencing data into actionable genomic insights, including QC, FASTQ/BAM/VCF generation, germline and somatic variant annotation, CNVs, SVs, joint genotyping, and gVCF outputs, with flexible analysis packages.
Whitepaper
Signios Bio Comprehensive Variant Detection
Learn about our computational precision pipelines, gold-standard GATK workflows, and how we transition raw reads into publication-ready, annotated biological insights.
Applications of Whole Exome Sequencing
Our whole exome sequencing services support a broad range of research applications, including:
Germline and Somatic Variant Detection
Identifying inherited and acquired genetic variations.
Targeted Discovery
Focusing on protein-coding regions where most disease-associated variants occur.
Rare Disease Research
Identifying causative mutations in complex phenotypes.
Oncology & Tumor Profiling
Detecting somatic variants and driver mutations.
Pharmacogenomics
Understanding how genetic variation impacts drug response.
Population Genetics
Large-scale cohort studies for genomic discovery.
Unlock the Full Potential of Your Data
Stop struggling with pipeline bottlenecks and schedule a technical consultation with our bioinformatics team to get your raw data to publication-ready insights today.
Frequently Asked Questions
What WES pipelines does Signios Bio use?
We utilize industry-standard workflows accelerated by Sentieon computational engines. Our validated workflows include high-stringency BWA-MEM alignment, Haplotyper for germline variants, and Strelka paired with LoFreq for somatic mutation profiling. We support reference mapping configurations for both hg19 and hg38 assemblies.
Can Signios Bio analyze third-party WES data?
Yes. Our bioinformatics team can seamlessly ingest external FASTQ or BAM files generated by any sequencing provider. We provide comprehensive secondary and tertiary analysis tailored to your specific raw data inputs, including alignment refinement, variant calling, and downstream functional annotations.
What are the WES analysis deliverables?
All analysis outputs are provided (BAM, VCF and more) based on the package chosen along with a publication-ready
Standard analysis
All items in *Basic Analysis +
- Alignment (BAM) file
- Germline VCF
- Germline variant annotation
- Low frequency germline variant calling
- Low frequency germline variant annotation
Advanced analysis
All items in Standard Analysis +
- All items in Standard Analysis +
- Somatic mutation annotation
- Low frequency somatic variant calling
- Low frequency somatic variant annotation
- Joint genotyping
- Structural variant calling
- Tumor/normal CNV calling
- gVCF
Specialized analysis
- Create a custom package to fit your project
- Custom analysis based on project requirements at an hourly rate
Basic Analysis*
* Data QC report, Raw data FASTQ file
Somatic mutation and TMB analysis supported?
Yes. We offer advanced somatic profiling, including tumor-normal subtraction, Tumor Mutational Burden (TMB) calculation, and log2-ratio Copy Number Variation (CNV) identification via ONCOCNV metrics. Our multi-caller pipeline is optimized to isolate rare, ultra-low frequency variants.
What species are supported for exome analysis?
Our production bioinformatics pipelines are fully optimized for both Human and Mouse exomes. Additionally, our team provides custom, bespoke analysis configurations for Rat and Non-Human Primate (NHP) architectures utilizing the latest reference assemblies.
How is data transferred and stored securely?
We prioritize data integrity using AES-encrypted, AWS-based cloud architectures and secure transfer protocols like SFTP or BaseSpace. All research datasets are handled under strict confidentiality guidelines and are restricted solely to authorized project teams.
Can I customize the variant filtering parameters?
What is WES analysis used for?
WES is ideal for identifying the molecular drivers of complex genetic diseases and cancers. While standard approaches only uncover foundational germline mutations, our advanced pipelines handle deep tumor-normal matching to provide comprehensive reporting for Germline Variant Calling, Somatic Mutation Profiling, and TMB Analysis—and our expert team is ready to help you seamlessly execute these workflows for your cohort today.
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Ready to Advance Your Discovery?
Don’t let complex data slow your research. Connect with our scientists to optimize your variant calling strategy and streamline your path to actionable genomic insights.