Prints the alignment in something similar to the samtools pileup format.
|--out||PrintStream||stdout||An output file created by the walker. Will overwrite contents if file exists|
|--showVerbose||boolean||false||Add an extra verbose section to the pileup output|
|--metadata||List[RodBinding[Feature]]||||Add these ROD bindings to the output Pileup|
Add these ROD bindings to the output Pileup. --metadata binds reference ordered data. This argument supports ROD files of the following types: BCF2, BEAGLE, BED, BEDTABLE, EXAMPLEBINARY, GELITEXT, OLDDBSNP, RAWHAPMAP, REFSEQ, SAMPILEUP, SAMREAD, TABLE, VCF, VCF3
An output file created by the walker. Will overwrite contents if file exists.
Add an extra verbose section to the pileup output. In addition to the standard pileup output, adds 'verbose' output too. The verbose output contains the number of spanning deletions, and for each read in the pileup it has the read name, offset in the base string, read length, and read mapping quality. These per read items are delimited with an '@' character.
GATK version 2.3-9-ge5ebf34 built at 2013/01/11 22:47:55.