This is the maskRepetitiveRegions command of dentist.
Options for the collectPileUps command.
Mask reference regions where the alignment coverage is not within set limits. This helps to identify repetitive or bad quality regions.
This class comprises the collectPileUps step of the dentist algorithm
Construct a stage of the repeat mask assessment pipeline.
Execute the collectPileUps command with options.
A RepeatAssessor should generate a repeat mask derived from a set of alignment chains.