Copy Number Variation (CNV) visualizer

Question

[waleed.a.osman]

Hi,

I would like to know if there is a CNV visualiser which will allow me to visualize CNVs on a per gene or per chromosome level.

Thanks

[German.M.Demidov]

one can always create a .seg file and make a track for IGV

https://software.broadinstitute.org/software/igv/SEG

Answer 1

[cmdcolin]

here is a list of tools I curate for visualizing CNVs https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag=CNV other tags like coverage and general-purpose genome browsers may also be relevant https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag=General https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag=Coverage (just added pierre's tool also:))

Answer 2

[Pierre Lindenbaum]

I wrote http://lindenb.github.io/jvarkit/CoveragePlotter.html

usage

java -jar dist/coverageplotter.jar -R src/test/resources/rotavirus_rf.fa --region "RF01:100-200" src/test/resources/*.bam 

Reviewing another set of ~100 SV/CNV pic.twitter.com/I4FSPSaksB

— Pierre Lindenbaum (@yokofakun) August 22, 2022

for large CNV I also wrote: http://lindenb.github.io/jvarkit/WGSCoveragePlotter.html

I need a screenshot, thank you twitter. pic.twitter.com/3RRMHcemJS

— Pierre Lindenbaum (@yokofakun) November 26, 2020