Subcommands

This section provides detailed documentation for each subcommand in MACS3. Use macs3 --help to see the list of subcommands.

• callpeak
  • Overview
  • Essential Commandline Options
  • Output files
  • Cutoff Analysis
• callvar
  • Overview
  • Detailed Description of usage
  • Command Line Options
  • Example Usage
  • callvar Algorithm
  • Customized fields in the Output VCF file
• hmmratac
  • Description
  • Output
  • Essential Options
  • Choices of cutoff values
  • Tune the HMM model
• bdgbroadcall
  • Overview
  • Detailed Description
  • Command Line Options
  • Example Usage
• bdgcmp
  • Overview
  • Detailed Description
  • Command Line Options
  • Example Usage
• bdgdiff
  • Overview
  • Detailed Description
  • Command Line Options
  • Example Usage
  • Step-by-step Instruction for calling differential peaks
• bdgopt
  • Overview
  • Detailed Description
  • Command Line Options
  • Example Usage
• bdgpeakcall
  • Overview
  • Detailed Description
  • Command Line Options
  • Example Usage
  • Cutoff Analysis
• cmbreps
  • Overview
  • Detailed Description
  • Command Line Options
  • Example Usage
• filterdup
  • Overview
  • Detailed Description
  • Command Line Options
  • Example Usage
• pileup
  • Overview
  • Detailed Description
  • Command Line Options
  • Example Usage
• predictd
  • Overview
  • Detailed Description
  • Command Line Options
  • Example Usage
• randsample
  • Overview
  • Detailed Description
  • Command Line Options
  • Example Usage
• refinepeak
  • Overview
  • Detailed Description
  • Command Line Options
  • Example Usage