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Source - BedOptions
- Options for specifying a BED file of target regions.
- OutputPrefixOptions
- Options for specifying the output path prefix (for commands that produce
multiple output files with shared prefix, e.g.
simulate). - ReferenceOptions
- Options for specifying the reference FASTA file.
- SeedOptions
- Options for controlling the random seed.
- VcfOptions
- Options for specifying an input VCF file and optional sample selection.
- CORE_OPTIONS
- Help heading for core options shared by most commands.