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, pVAAST, PHEVOR, GEMINI, and IOBIO
- Reference-free variant calling and investigation of de novo variants using RUFUS
- Structural variant calling and prioritization using Lumpy and WHAM
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 90 days after analyses are complete, and help with transfer to a final storage solution after project completion. Our variant calling pipeline uses a GATK-based variant calling software, and includes WHAM for structural variant calling, as well as standard QC metrics (FastQC, samtools stats, samtools flagstat, bcftools stats, goleft). You will receive polished, lossless BAM files, gVCF files, and finalized VCF files. University of Utah investigators will access their data via GnomEx 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) |
| # sequences |
1-100 |
101-500 |
>500 |
| WGS (60X) |
$52.0 |
$46.8 |
$42.1 |
| WGS (30X) |
$48.0 |
$43.2 |
$38.9 |
| WES |
$26.0 |
$20.8 |
$16.6 |
| Panel |
$19.5 |
$15.6 |
$12.5 |
|
|
|
|
|
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 $8,877 per month (minimum project is 0.25 months). 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.
Joint genotyping
We can jointly genotype data across separate projects/datasets where variant calling has already been done. The charge for this service is $0.51 per genome sequence with a minimum charge of $127.
Project management
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 is $0.64 per genome sequence with a minimum charge of $159 per dataset.
