I mapped the NGS whole genome sequencing reads to reference genome sequence, to detection natural variations of CDS region. To filter out some protein coding genes might with negative deletion calling, I want to get the coverage of every deletion variation. Like if there there are 5 reads go cross an deletion, I expect the depth would be 5.
I tried "samtools depth", but it would not give the expected result. If all the reads confirm a deletion, the samtools would output the depth as 0.
Any idea to do that please?