I am working with targeted amplicon sequencing data for 200 samples! I want to calculate the average depth per amplicon? I tried bedtools coverage, but it gives total number of reads which map to the target region and I am not sure if that is the average depth. It is little confusing to me.
/home/tools/bedtools2/bin/bedtools coverage -a ../../amplicon_coords.bed -b sample1_RG_sorted_indexed.bam
Is there any other way or any modified way to use bedtools coverage option to calculate the average depth per amplicon?
Any help will be appreciated.