Trouble running ExomeDepth

[hazmup]

I am having some problems with ExomeDepth. I have a batch of 6 unrelated exomes and for each one 3-5 are selected in the reference set. There are thousands of CNVs called for all samples, with very large BFs.
I am using ExomeDepth with a hg38 exons bed file, which I got from the UCSC knownGene table. I am then discarding alternative, and sex chromosomes and switching to 'chr' convention.

(Plus, there seems to be some formatting issue in the .csv file (sample attached).
sample.xlsx)