ValidatingPileup

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.

Category Quality Control and Simple Analysis Tools

Introduction

Samtools' pileup data should be specified using the command-line argument '-pileup:SAMPileup '.

ValidatingPileup specific arguments

Name	Type	Default value	Summary
Required
--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
Optional
--continue_after_error	boolean	false	Continue after an error

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

--continue_after_error ( boolean with default value false )

Continue after an error.

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

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

--pileup ( required RodBinding[SAMPileupFeature] )

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.