Given two BAMs with different read groups, it compares them based on ReduceReads metrics.
This is a test walker used for asserting that the ReduceReads procedure is not making blatant mistakes when compressing bam files.
Two BAM files (using -I) with different read group IDs
java -jar GenomeAnalysisTK.jar -T $WalkerName
These Read Filters are automatically applied to the data by the Engine before processing by CompareBAM.
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).
This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.
|--reduced_readgroup||String||NA||The read group ID corresponding to the compressed BAM being tested|
|--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.|
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.
Minimum base quality to be considered..
Minimum mapping quality to be considered..
The read group ID corresponding to the compressed BAM being tested.
Test if the base counts tag in consensus reads are accurate..
Test if the bases marked as '=' are indeed ref bases..
GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.