this document looks at the depth at a particular position in a BAM file a user sent me, at position 14712.
I discuss in the comments what settings might be related to the coverage differents
The major variables between tools and the scores they report for coverage are related to the filters that are by default applied. Tools that report a lower score generally include duplicate and qc vendor fail filters by default. In this test at a particular position, these tools reported 74 reads.
Scores that are higher have no filters applied. In this test at a particular position, these tools reported 423.