At every locus in the input set, compares the pileup data (reference base, aligned base from each overlapping read, and quality score) to the reference pileup data generated by samtools.
These Read Filters are automatically applied to the data by the Engine before processing by CheckPileup.
This tool can be run in multi-threaded mode using this option.
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.
|--pileup||RodBinding[SAMPileupFeature]||NA||The SAMPileup containing the expected output|
|--out||PrintStream||stdout||An output file created by the walker. Will overwrite contents if file exists|
|--continue_after_error||boolean||false||Continue after an error|
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.
Continue after an error.
An output file created by the walker. Will overwrite contents if file exists.
The SAMPileup containing the expected output. --pileup binds reference ordered data. This argument supports ROD files of the following types: SAMPILEUP
GATK version 2.8-1-g2a26ec9 built at 2013/12/06 16:54:02.