VizCNV - An integrated platform for concurrent phased BAF and CNV analysis

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This is a shiny app for chromosomal copy number variant analysis. It can parse the vcf file with SV calls, visualize CNV and B-allele frequency and genetic phasing information interactively.

# quick start
shiny::runGitHub(repo = "BCM-Lupskilab/VizCNV",ref="main")

Download current version

Pull docker image

Q&A

Prerequisites

R version >= 4.2 Following R libraries are required: Shifting level models based segmentation is performed using SLMSuite.

Citation

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Please cite the following article if you use VizCNV in your research:

• Du, H., Jolly, A., Grochowski, C. M., Yuan, B., Dawood, M., Jhangiani, S. N., Li, H., Muzny, D., Fatih, J. M., Coban-Akdemir, Z., Carlin, M. E., Scheuerle, A. E., Witzl, K., Posey, J. E., Pendleton, M., Harrington, E., Juul, S., Hastings, P. J., Bi, W., … Liu, P. (2022). The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation. Genome Medicine, 14(1), 122. https://doi.org/10.1186/s13073-022-01123-w
• Du, H., Lun, M. Y., Gagarina, L., Bengtsson, J. D., Grochowski, C. M., Mehaffey, M. G., Hwang, J. P., Jhangiani, S. N., Bhamidipati, S. V., Muzny, D. M., Poli, M. C., Ochoa, S., Chinn, I. K., Lindstrand, A., Posey, J. E., Gibbs, R. A., Liu, P., Lupski, J. R., & Carvalho, C. M. B. (2025). An integrated platform for concurrent structural and single-nucleotide variants improves copy-number detection and reveals pathogenic alleles in undiagnosed Mendelian families. Genome Medicine, 18(1), 16. https://doi.org/10.1186/s13073-025-01593-8