Germline Variant Calling : 30X WGS
Germline Variant Calling (30X WGS/WES)
End-to-end, scalable genomic analysis for research and biotech teams
Accelerate discovery with a fully integrated germline variant calling solution, from sequencing to analysis-ready results. C3G offers validated pipelines, secure infrastructure, and expert support to help you extract high-confidence variants from large-scale genomic datasets.
Who is this ideal for?
Biotech companies
Who are scaling genomic discovery pipelines
Clinical research teams
Who are analyzing WGS/WES cohorts
Academic labs
Who are lacking local bioinformatics infrastructure
Population genomics and rare disease studies
The Challenge
Managing and analyzing large-scale genomic datasets can be a major hurdle for academic labs or smaller biotech companies. They often hit the same walls before they even get to reach interpretation, such as:
- Massive data, limited infrastructure. WGS projects generate terabytes per cohort and need storage and compute power.
- A lack of infrastructure to efficiently process, store, and explore these datasets can slow analysis and discovery.
- Scarce bioinformatics expertise. Building and maintaining accurate, reproducible variant-calling pipelines requires specialists who are hard to hire and retain.
- Signal versus noise. Distinguishing true biological variants from sequencing artifacts and identifying clinically relevant mutations is a hurdle in interpretation.
Our solution
C3G’s germline variant calling solution covers the full journey, from sample intake to high-confidence, annotated variant calls. Sequencing, bioinformatics, and interpretation support sit under one roof, so your team doesn’t have to coordinate vendors, stand up infrastructure, or hire specialists. You partner with expert C3G bioinformaticians running the analysis, from the first consultation through delivery and training.
How it works:
Consultation
We begin with a dedicated call to define your sequencing strategy, study design, budget, and data analysis requirements.
Sample processing & sequencing
Samples are received by the McGill Genome Centre, where they undergo quality control, library preparation, and high-throughput sequencing.
Bioinformatics analysis
Your data is processed using the GenPipes DNA-seq pipeline, including alignment, variant calling, filtering, and annotation.
Data delivery & access
We provide secure delivery of raw data, alignments, and variant calls, along with access credentials for your team.
Training & support
You receive a one-hour onboarding session with C3G experts to guide data interpretation and support downstream analyses.
Looking for a more in‑depth look at how this process works?
Explore our case study to see how this solution supports you every step of the way!
Deliverables
- Sequencing data: 30X short-read WGS with QC validation at intake and post-sequencing
- Processed data: fully trimmed, aligned, sorted, deduplicated, and compressed files
- Quality control: expert-reviewed QC reports and summary statistics
- Variant calling: consensus approach using multiple tools to reduce false positives
- Filtered outputs: curated and processed VCF files ready for downstream analysis
- Analysis tools: robust filtering, sorting, and data manipulation capabilities
- Expert insight: actionable interpretation and guidance on results
- Training: onboarding session covering filtering, PCA, and burden testing
- Ongoing support: continued access to C3G expertise after delivery
Why C3G?
C3G brings over a decade of experience delivering high-quality, large-scale genomics analysis, with a focus on accuracy, reliability, and reproducibility. Our expert bioinformatics team combines deep technical expertise with validated workflows to minimize errors and ensure consistent results.
With dedicated project workspaces, controlled data access, and integrated analysis tools, C3G streamlines the data lifecycle, allowing teams to focus on discovery rather than infrastructure.
The result: faster insights, reduced operational burden, and scalable, secure genomics workflows.
Get started today!
Ready to scope your next sequencing project? A C3G expert will walk you through the study design, timeline, and budget.
Contact: ryan.borotra@mcgill.ca