Visualising a bam file with multiple genomes

Question

[Daksh]

Hey,

I want to visualise a bam file with multiple genomes. I sorted it using samtools and got an index file too.

I tried Qualimap first, but when the coverage across reference was produced, it was not coming out well as the values were getting overlapped towards the end of the axes.

I need to get a better visualisation. I used various tools, IGV, GenomeWorkbench and even ngscat, but a lot of these tools do not accept my bam file since it has several/multiple types of genome (viral and human). I need a tool which would accept it and give me a cleaner graph

Thanks!

Answer 1

[Pierre Lindenbaum]

see How to plot coverage and depth statistics of a bam file ; Coverage plot of a complete genome

[Daksh]

Thanks Pierre, I'm pretty new to coding, so could you help me out with your tool jvarkit and wgscoverageplotter?

Im working on macOS, so downloading the file was not an issue. However, when I try to call it using wgscoverageplotter it says command not found. (even though I am in that directory)

Also, when I will be able to call it, I am unsure how to put my file through the plotter. Could you help me out with this?

[Pierre Lindenbaum]

when I try to call it using wgscoverageplotter it says command not found.

http://lindenb.github.io/jvarkit/WGSCoveragePlotter.html#download-and-compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew wgscoverageplotter
$ java -jar dist/wgscoverageplotter.jar ....