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Validates consistency of the aligner interface

Category Diagnostics and Quality Control Tools

Traversal ReadWalker

PartitionBy READ


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.


This tool requires that BWA be available on the java path.

Additional Information

Read filters

This Read Filter is automatically applied to the data by the Engine before processing by CheckAlignment.

Downsampling settings

This tool does not apply any downsampling by default.

Command-line Arguments

Inherited arguments

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 is an Engine capability and is therefore available to all GATK walkers).

CheckAlignment specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s) Default value Summary
Optional Parameters
NA Index files generated by bwa index -d bwtsw

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

--BWTPrefix / -BWT

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


See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.1-1-g07a4bf8 built at 2014/03/18 07:00:36. GTD: NA