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.
|--out||PrintStream||stdout||An output file created by the walker. Will overwrite contents if file exists|
|--pileup||RodBinding[SAMPileupFeature]||NA||The SAMPileup containing the expected output|
|--continue_after_error||boolean||false||Continue after an error|
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 2.3-9-ge5ebf34 built at 2013/01/11 22:47:55.