Pileup

Prints the alignment in something similar to the samtools pileup format.

Category Quality Control and Simple Analysis Tools

Introduction

Each line represents a genomic position, consisting of chromosome name, coordinate, reference base, read bases, and read qualities. Associated command: samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list] [-iscg] [-T theta] [-N nHap] [-r pairDiffRate]

Pileup specific arguments

Name	Type	Default value	Summary
Required
--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
Optional
--metadata	List[RodBinding[Feature]]	[]	Add these ROD bindings to the output Pileup

Additional capabilities

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 capability is available to all GATK walkers.

CommandLineGATK

Argument details

--metadata / -metadata ( List[RodBinding[Feature]] with default value [] )

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

--out / -o ( PrintStream with default value stdout )

An output file created by the walker. Will overwrite contents if file exists.

--showVerbose / -verbose ( boolean with default value false )

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.