Overview
From raw reads to research-ready variants.
We specialize in variant calling and disease-gene discovery using tools developed by the Utah Center for Genetic Discovery — including VAAST, PHEVOR, VIQ, Smoove, Slivar, RUFUS, IOBIO, and others.
Operating as a fee-for-service internal spinout of the UCGD academic initiative, the Core makes our resources and expertise available to any Utah investigator while providing a mechanism for cost recovery and infrastructure funding. The administrative and technical infrastructure supports more collaborators and projects than can be managed by individual investigators alone.
What we do
Services
Long & short read alignment + variant calling
For NGS datasets including whole genome, whole exome, and panel sequences.
Joint genotyping
Joint genotyping of separate datasets and controls for cohort-level analyses.
Disease-gene discovery
Cohort and family analyses using VAAST, PHEVOR, VIQ, Slivar, and IOBIO.
VAAST PHEVOR VIQ Slivar IOBIO
Reference-free variant calling
Investigation of de novo variants using RUFUS.
RUFUS
Structural variant calling & prioritization
Using Smoove and Manta for SV discovery across short-read sequencing data.
Smoove Manta
Pathogenic repeat expansion identification
STR genotyping and detection of expansions in disease-associated loci.
Methylation analysis
Long-read methylation profiling using PacBio and ONT sequencing data.
RNA-seq & scRNA-seq
Bulk and single-cell transcriptomic analysis pipelines.
Microbial genome assembly
Assembly and annotation pipelines for microbial isolates.
Metagenomic analysis
Metagenomic profiling and taxonomic classification using MultiQC and our internal stack.
Genome annotation
Gene model prediction, functional annotation, and quality assessment.
Project & data management
End-to-end project management through the Mosaic Data Portal.
Mosaic
Rates
Variant calling rates.
Per-sample variant calling
Whole genome & exome rates
Output formats
What you receive.
University of Utah investigators see their data via Mosaic or directly on CHPC. Data sharing for external projects is determined on an individual basis. For external academic and commercial rates, contact Carson Holt at carson.holt@genetics.utah.edu.
Post-VCF research analyses
Discovery analyses downstream from variant calling, performed by analysts collaborating with researchers studying inherited disorders, lung & heart disease, inflammatory and immune conditions, metabolic disease, and neurological conditions.
Custom development
Our team can also assist with custom software and workflow development at the same hourly rate.
Joint genotyping
Joint genotyping data across separate projects/datasets where variant calling has already been done. $230 setup, then $2.00 per sample.
Data storage & project management
Storage built for genomic- scale data.
The UCGD Core has purchased 4.4 PB of high-performance (300 GB/s) Lustre storage to support research projects at the University of Utah. This equipment is situated at the University’s downtown datacenter inside CHPC’s HIPAA-compliant Protected Environment, and can be accessed from all nodes in the Redwood HPC cluster.
The storage is optimized for data-intensive applications such as genomic analysis. The purchase of this equipment was made possible by an NIH S10 instrumentation grant (S10OD034321).
If your research requires storing large volumes of data or you have high- performance I/O read/write requirements, contact the UCGD Core to discuss provisioning space on the Lustre system. NIH-funded projects can be provisioned up to 100 TB of storage space at no charge depending on project needs.
Additional data backup services and access to the Mosaic web-based data management portal are also available through the UCGD core for $85/TB per year. Note that WGS, WES, and RNA samples processed through the UCGD Core already include 1 year of data storage, backup, and Mosaic access as part of the per-sample billing rate.
Forms & submission
Start a project.
Need more detail? Our Core Documentation Portal walks through the full submission lifecycle from authorization to data delivery, including expected timelines and project scoping.
Referencing us
If we contributed, cite us.
[Service type] was performed at the Utah Center for Genetic Discovery Core Facility, part of the Health Sciences Center Cores at University of Utah. The support and resources from the Center for High Performance Computing at the University of Utah are gratefully acknowledged. The computational resources used were partially funded by the NIH Shared Instrumentation Grants S10OD034321 and S10OD021644.
Nodira Codell, MPA
nodira.codell@genetics.utah.edu
801.581.7405
Utah Center for Genetic Discovery
