Pacbio Longread Depth of coverage

Question

[hellbio]

How to calculate the depth of coverage on a BAM file generated from Pacbio Targeted Longread sequencing?

In short-read paired-end sequencing, GATK DepthofCoverage gives the fraction of coverage of each interval in the bed file at 10X,30X,50X etc.

How to generate similar coverage metrics from PacBio BAM file? Would be helpful if someone could suggest some tools or commands to achieve this.

[GenoMax]

Coverage calculation should be the same for any kind of sequencing.

Answer 1

[Huiyang]

Try PanDepth, it supports both short reads and long reads of types HIFI/CLR/ONT.

Answer 2

[Bas]

You could try mosdepth, which is used by PacBio's HiFi-human-WGS-WDL workflow.