I'm looking for a nice way to calculate the percentage of reads on specifique chromosomes (MT und (1-23,X,Y) und unplaced scaffold).
I know I can get the read counts per chromosome with
samtools idxstats, however I have a lot of bam files and I would like to automate the calculation. The problem is, I'm struggling with basic batch text maniplulation and would therefore appreciate any help you can give me (specific or general).
Edit: I forgot to mention, that I have multiple bam files, which are indexed and only consist of uniquely mapped reads.