Copy Number Variation (CNV) visualizer
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5 months ago

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

Copy-Number-Variation CNV visualization • 504 views
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one can always create a .seg file and make a track for IGV

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

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5 months ago

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 

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

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5 months ago
cmdcolin ★ 2.7k

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:))

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