Table 1.

Comparing the software tools of coverage calculation

Performance	Samtools	BEDTools	Sambamba	Mosdepth	Megadepth	BamToCov	PanDepth
Input
Sorted bam	√	√	√	√	√	√	√
Sorted cram	√	√	✕	√	√	√	√
Unsorted bam	✕	✕	✕	✕	✕	✕	√
Unsorted cram	✕	✕	✕	✕	✕	✕	√
GFF	✕	✕	✕	✕	✕	√	√
GTF	✕	✕	✕	✕	✕	√	√
BED	✕	√	√	√	√	√	√
Window size	✕	√	√	√	√	✕	√
Filtering
Mapping quality	√	✕	√	√	✕	√	√
Flag	√	✕	√	√	✕	√	√
Output
Covered site	√	✕	✕	✕	✕	✕	√
Total depth	√	√	√	√	√	√	√
GC (%)	✕	✕	✕	✕	✕	✕	√
Coverage (%)	√	✕	✕	✕	✕	✕	√
Mean depth	√	✕	✕	√	✕	√	√