Why coordinate sort is required in sambamba depth?

Question

[MobiusT]

When I run the command

sambamba depth base -L genomicdataset001.bed $filename

It gives the following error

sambamba-depth: All files must be coordinate-sorted

Why coordinate-sort is required in this run and what coordinate sorting is exactly?

Answer 1

[Pierre Lindenbaum]

what coordinate sorting is exactly?

samtools sort bam file

Why coordinate-sort is required

coordinate sort is de facto the simplest way to know how many read overlap a region.

and now, review and/or validate all your previous questions: How to use minimap2? ; How a fastq.gz file is formatted? ; What is read depth exactly? ; Samtools index and sambamba-depth error? ; sambamba-depth: All files must be coordinate-sorted error? ...