Plot percentage of genome covered Given a aligned bam file (wgs/bwa-mem) what steps do i need to perform to generate a plot as seen below (from this paper):



We are trying to see how much of genome was covered using pacbio and illumina for cow.



You mean remove this left plot?
The general steps are:


Install deepTools
Run plotCoverage on your BAM files
Remove the left-most plot in photoshop/gimp/imagemagick