PrintRODs

Prints out all of the RODs in the input data set.

Category Quality Control and Simple Analysis Tools

Introduction

Data is rendered using the toString() method of the given ROD.

PrintRODs specific arguments

Name	Type	Default value	Summary
Required
--input	RodBinding[Feature]	NA	The input ROD which should be printed out.
--out	PrintStream	stdout	An output file created by the walker. Will overwrite contents if file exists

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

--input / -input ( required RodBinding[Feature] )

The input ROD which should be printed out.. --input 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.

GATK version 2.3-9-ge5ebf34 built at 2013/01/11 22:47:55.