Parsing SAM/BAM files for additional information I used BWA-MEM to alignment and I would like to gather the some informations like total % of match, mismatch, insert/delete etc. I am wondering if there is any existing tools that produces this information?
Other options... samtools stats maybe gives you some of the stats you are after. Chances are you already have samtools so nothing additional to install. Also useful may be pysamstats, in particular the variation sub-command.