The Utah Center for Genetic Discovery helps investigate the genetic basis for human disease by providing whole exome and whole genome sequence analyses for research and clinical projects. We specialize in variant calling and disease-gene discovery utilizing tools developed by the Utah Center for Genetic Discovery, including VAAST, PHEVOR, VIQ, Smoove, Slivar, RUFUS, IOBIO, and others.

For general inquiries, price quotes, and timeline estimates, please contact Carson Holt at carson.holt@genetics.utah.edu 

A work authorization form is required before projects can be submitted for service.

On-Campus Form: On-Campus Form 

Off-Campus Form: Off-Campus Form 

How-to Video: How-to Video 

New project submission portal: REDCap 

More Information: Core Documentation Portal

• Long read and short read alignment and variant calling for NGS datasets, including whole genome, whole exome, and panel sequences
• Joint genotyping of separate data sets and controls
• Disease gene discovery in cohorts and families using VAAST, PHEVOR, VIQ, Slivar, and IOBIO
• Reference-free variant calling and investigation of de novovariants using RUFUS
• Structural variant calling and prioritization using Smoove and Manta
• Pathogenic repeat expansion identification
• Methylation analysis using long read PacBio and ONT sequencing data
• RNA-seq and scRNA-seq analysis
• Microbial genome assembly
• Metagenomic analysis and taxonomic classification
• Microbial genome assembly
• Genome Annotation
• Project and data management through the Mosaic platform

Variant calling  

Variant calling rates include consult time with our bioinformatics team to determine your analysis needs, receipt of data from sequencing vendor, storage and access to your data on our equipment at CHPC for 1 year and help with transfer to a final storage solution after project completion.  Our variant calling pipeline uses Sentieon (a GATK-equivalent software package), and includes Smoove and Manta for structural variant calling, as well as standard QC metrics (FastP, bcftools stats, alignstats, goleft, peddy, and MultiQC).  You will receive polished, lossless CRAM files, gVCF files, and finalized VCF files.  University of Utah investigators will access their data via Mosaic or directly on CHPC servers.  Data sharing method for external projects is determined on an individual basis.

Variant calling (Minimum charge of $230)

Internal variant calling rates:

For external academic and commercial rates, please contact Carson Holt carson.holt@genetics.utah.edu.

Our team of research analysts are available to help you with a variety of discovery analyses downstream of variant calling at the rate of $115 per hour. Our analysts benefit from collaboration with a dynamic team of researchers, clinicians, and software developers studying a broad range of inherited disorders including lung and heart disease, inflammatory and immune conditions, metabolic disease, and neurological conditions.  Analyses to be performed and total analyst time needed for your project will be determined on an individual basis after consultation with our team.

Our team can also assist with custom software and workflow development at a rate of $115 per hour.

We can jointly genotype data across separate projects/datasets where variant calling has already been done.  The charge for this service is $230 for project setup then $2.00 per sample.

The Utah Center for Genetic Discovery (UCGD) Core has purchased 4.4PB of high performance (300Gb/s) Lustre data storage to support research projects at the University of Utah. This equipment is installed at the university’s downtown datacenter inside CHPC’s HIPAA compliant Protected Environment, and it can be accessed from all nodes in the Redwood HPC cluster. This 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 IO read/write requirements, please contact the UCGD Core to discuss provisioning space on the Lustre data storage system. NIH funded projects can be provisioned up to 100TB of storage space at no charge depending on the needs of a project. 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 though the UCGD Core already includes 1 year of data storage, backup, and Mosaic access as part of the per sample billing rate.

Please acknowledge our contribution to your research by including this statement in all publications:

(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.