I know how to calculate the coverage and depth stats using various tools, but I haven’t been able to find a way to plot these!
I came across a tool called BAMStats, but I had way too many input files for the tool to work. Any help would be greatly appreciated. Thanks!
I have had good experience with qualimap:
It can use multiple threads to iterate through your bam files and can efficently pull out a number of useful alignment and coverage statistics. It will make some plots for you, or you can use http://multiqc.info/ to plot results from a number of datasets with minimal effort.
Works very well, thank you!