We use bamtobed to covert bam files to bed files. I am wondering if the output is sorted by default , because our output bed files seems to be sorted by chromosome and position. I am asking this question because we are using bedtools to calculate coverage with large bam files which takes up a lot of memory. It was suggested to pre-sort the bed files before running bedtools coverage in the documentation to help reduce the memory usage. However, sorting on bash , even running parallel with 8 cores, is still time-consuming. So, it would be great if anyone can confirm bamtobed does that already .