Hello,

I would like to get the coverage for every single base in all regions in a bed file. For this I use samtools now

`samtools depth -aa -b regions.bed input.bam`

This all works as excpected. But the more regions I have the longer this tasks takes of course. I can speed it up by dividing the bed file and start parallel processes. But it still needs about 45min to complete. My whole analyse pipeline from fastq to an annotated vcf file runs only 1h for this data set.

So I wonder if there is a faster way for this task?

fin swimmer
Try bedtools coverage with -d option ([link][1])

(And do notice the first note on *-sorted*)

  [1]: http://bedtools.readthedocs.io/en/latest/content/tools/coverage.html