UCGD SERVICE RECHARGE CENTER

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Overview

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 

Services

  • 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
  • Project and data management through the Mosaic platform

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

Rates

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.

Internal variant calling rates:

      Variant calling rate (per sequence) 
 # sequences1-100101-500501-10001001-2000>2000 
WGS (60X)$53$43$33$24$15
WGS (30X)$48$38$29$20$12
WES$29$19$16$13$10 
Panel$27$17$14$11$9 

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

Post-VCF research analyses

Our team of research analysts are available to help you with a variety of discovery analyses downstream of variant calling at the rate of $68 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.

Custom Development

Our team can also assist with custom software and workflow development at a rate of $80 per hour.

Joint genotyping

We can jointly genotype data across separate projects/datasets where variant calling has already been done.  The charge for this service is $150 for project setup then $0.73 per sample.

Project management/Storage only Projects

Our team can help you transfer data to/from collaborators, and host and store your data sets on our equipment at CHPC.  The charge for this service $129 for project setup then $30 per terabyte per year of data storage.

DNA Sequencing Through ARUP Laboratories

We can facilitate return of DNA sequence data from ARUP Laboratories. Sequencing data that is not pushed through our variant calling pipeline will be billed as a “storage only” project. Please contact Devin Close at ARUP (devin.close@aruplab.com) for estimates of sequencing costs.

Referencing us

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 Service Recharge Center, 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.