Calculate Average Genome Coverage Accurately for hg38 Reference Using Alternate Contigs and Decoys

Question

[dario.garvan]

I have whole genome sequencing data aligned to hg38 and alternate contigs and decoys (the one from bwakit). What command could I use to accurately calculate the average genome coverage of each BAM file?

[ATpoint]

Tools To Calculate Average Coverage For A Bam File? and the search function please. Has been asked many times before.

[dario.garvan]

Yes, but I don't think any of those tools explicitly handle the case of alternate contigs. Somehow, the main chromosome and its alternate contigs need to be merged before calculation happens. Otherwise, the coverage of the main chromosome is artificially reduced if the reads map to alternate contigs.