Test routine for new VariantContext object
These Read Filters are automatically applied to the data by the Engine before processing by CompareCallableLoci.
This tool applies the following downsampling settings by default.
The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).
This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.
|--comp1||RodBinding[BEDFeature]||NA||First comparison track name|
|--comp2||RodBinding[BEDFeature]||NA||Second comparison track name|
|--out||PrintStream||stdout||An output file created by the walker. Will overwrite contents if file exists|
|--printstate||String||NA||If provided, prints sites satisfying this state pair|
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
First comparison track name. --comp1 binds reference ordered data. This argument supports ROD files of the following types: BED
Second comparison track name. --comp2 binds reference ordered data. This argument supports ROD files of the following types: BED
An output file created by the walker. Will overwrite contents if file exists.
If provided, prints sites satisfying this state pair.
GATK version 2.8-1-g2a26ec9 built at 2013/12/06 16:54:02.