Software Packages

Department of Quantitative Health Sciences
Mayo Clinic Research
Formerly known as the Department of Health Sciences Research

Related links: Division Overview R Shiny Applications


Structural Variations (SVs) and Copy Number Variations (CNVs) are the major source of genomic variations. CNVnator is a tool for Copy Number Variation (CNV) discovery and genotyping  from depth-of-coverage by mapped reads.  It accepts .bam files as input and generates CNVs calls in less than 10 hours of calculations.

The source code and extended descriptions are available here

By downloading the CNVnator software you agree to the terms of this Creative Commons license (Attribution-NonCommerical).

Latest release: CNVnator

When referencing CNVnator, please cite the most recent publication.

  • Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 2011 Jun;21(6):974-84.
  • Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO; 1000 Genomes Project. Mapping structural variation at fine scale by population scale genome sequencing. Nature. 2011 Feb 3;470(7332):59-65.

Page last modified: January 7, 2018