AlignmentValidation

Validates consistency of the aligner interface by taking reads already aligned by BWA in a BAM file, stripping them of their alignment data, realigning them, and making sure one of the best resulting realignments matches the original alignment from the input file.

Category Quality Control and Simple Analysis Tools

Introduction

AlignmentValidation specific arguments

Name	Type	Default value	Summary
Optional
--BWTPrefix	String	NA	Index files generated by bwa index -d bwtsw

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

--BWTPrefix / -BWT ( String )

Index files generated by bwa index -d bwtsw. The supporting BWT index generated using BWT.

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