For panes or exome sequencing data, use this command:
> MappingQC -in [bam] -roi [target_region] [options]
For whole genome sequencing data, use this command:
> MappingQC -in [bam] -wgs [options]
For transcriptome sequencing data, use this command:
> MappingQC -in [bam] -rna [options]
The full list of command-line parameters and changelog can be found here.