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.
R version >= 4.2 Following R libraries are required:
Shifting level models based segmentation is performed using SLMSuite.
Launch app on local with the main branch:
shiny::runGitHub(repo = "BCM-Lupskilab/VizCNV")or Launch app on local with the dev branch:
shiny::runGitHub(repo = "cluhaowie/VizCNV",ref="dev")A docker image is public available and can be pulled from docker hub
docker pull duclare123/vizcnv_dev
and run docker image with
docker run -d -p 3838:3838 -v /path/to/local:/root/input/ duclare123/vizcnv_dev
then accessing the app with http://localhost:3838/
Upload the required file from local file systerm: 
If launch the app on cloud or on server, input file need to be upload due to access restriction.
Visualize the CNV calls in table format, read depth plot and B-allele frequency together: 
The app require read depth file as the input: A output from mosedepth can be used example of generate the read depth file for 1Kb window size would be:
mosdepth -n --fast-mode --by 1000 sample.wgs $sample.wgs.cram