Coverage plot of a complete genome

Question

[frymor2]

In a paper I was reading i have found the attached image. It shows the duplication of specific chromosomes in different yeast strains after treatment with antibiotics.

I was wondering how can one plot the whole genome in such a way? Are there any tools or R packages to get such a result?

thanks

[German.M.Demidov]

tbh, it looks like a CNV caller worked here =) the plots looks too uniform - which means they were likely GC/library size normalized before plotting

or it is a rolling median across the coverage precalculated in some windows (e.g. 50kbps)

[scheitelt]

yes, This is true, but it doesn't really answer the question. The question was how this plot was done. can some please help me too?

[German.M.Demidov]

You can calculate the coverage per some window, smooth it with rolling median and plot in R - this is what I would do

Answer 1

[Pierre Lindenbaum]

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

[frymor2]

Thanks Pierre, this looks good. Is it possible to use a bam file with multiple read groups as an input here?

[Pierre Lindenbaum]

you meant that there is only more that one sample ? everything would be merged here, but I can add an option to only select a defined sample.

[frymor2]

What I meant is, if there is a possibility to take a bam file with multiple samples, defined by separate read groups and use it as an input. I have a concatenated bam files I have merged from several single samples, for several reasons. Now I would like to plot this bam file, but to get the coverage separated by the single samples (e.g marked by the read groups). This should be something like the the facet_wrap in the R command ggplot. One row should represent one read group instead of a whole bam file.

Would this be possible?

[Pierre Lindenbaum]

I've just added an option --samples http://lindenb.github.io/jvarkit/WGSCoveragePlotter.html

[frymor2]

thanks, I'll give it a go as soon as as possible and come back to you