Pacbio Longread Depth of coverage
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.
2 answers
You could try mosdepth, which is used by PacBio's HiFi-human-WGS-WDL workflow.
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