CompareBAM

Given two BAMs with different read groups, it compares them based on ReduceReads metrics.

Category Diagnostics and Quality Control Tools

Traversal LocusWalker

PartitionBy LOCUS

Overview

This is a test walker used for asserting that the ReduceReads procedure is not making blatant mistakes when compressing bam files.

Input

Two BAM files (using -I) with different read group IDs

Output

[Output description]

Examples

    java
      -jar GenomeAnalysisTK.jar
      -T $WalkerName

Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by CompareBAM.

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).

CommandLineGATK

CompareBAM specific arguments

This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.

Name	Type	Default value	Summary
Required
--reduced_readgroup	String	NA	The read group ID corresponding to the compressed BAM being tested
Optional
--min_base_qual	int	20	Minimum base quality to be considered.
--min_mapping_qual	int	20	Minimum mapping quality to be considered.
--test_base_counts	boolean	false	Test if the base counts tag in consensus reads are accurate.
--test_equal_bases	boolean	false	Test if the bases marked as '=' are indeed ref bases.

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.

--min_base_qual / -mbq ( int with default value 20 )

Minimum base quality to be considered..

--min_mapping_qual / -mmq ( int with default value 20 )

Minimum mapping quality to be considered..

--reduced_readgroup / -rr ( required String )

The read group ID corresponding to the compressed BAM being tested.

--test_base_counts / -tbc ( boolean with default value false )

Test if the base counts tag in consensus reads are accurate..

--test_equal_bases / -teq ( boolean with default value false )

Test if the bases marked as '=' are indeed ref bases..

GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.