FORUMCategory: BioinformaticsPlotting coverage and depth statistics of a BAM file
nibeh Staff asked 2 years ago



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!

1 Answers
Best Answer
rcorbett Staff answered 2 years ago



I have had good experience with qualimap:
http://qualimap.bioinfo.cipf.es/
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.

nibeh Staff replied 2 years ago

Works very well, thank you!