Walks over the input data set, calculating the total number of covered loci for diagnostic purposes.
This is the simplest example of a locus walker.
One or more BAM files.
Number of loci traversed. If an output file name is provided, then the result will be written to that file. Otherwise it will be sent to standard console output.
java -Xmx2g -jar GenomeAnalysisTK.jar \ -T CountLoci \ -R ref.fasta \ -I input.bam \ -o output.txt \ [-L input.intervals]
These Read Filters are automatically applied to the data by the Engine before processing by CountLoci.
This tool can be run in multi-threaded mode using these options.
This tool applies the following downsampling settings by default.
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 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|
|stdout||An output file created by the walker. Will overwrite contents if file exists|
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.
An output file created by the walker. Will overwrite contents if file exists
GATK version 3.0-0-g6bad1c6 built at 2014/03/06 06:38:04. GTD: NA