I've now read a number of posts on ways to calculate depth of coverage (for a gene, exon, etc..)
What I'm not clear about is - whether it's appropriate to count coverage with filters in place (i.e. gatk's depthOfCoverage uses a number of filters by default e.g. excluding duplicate reads, vendor quality failed reads, etc..)
If the objective of the exercise is to assess how well a particular sequencing technology is able to cover a region .. does It make sense to retain all reads? or filter out reads that meet criteria such as those applied by GATK?