Utility program to print a list of available annotations
This is a very simple utility tool that retrieves available annotations for use with tools such as UnifiedGenotyper, HaplotypeCaller and VariantAnnotator.
This is a command-line utility that bypasses the GATK engine. As a result, the command-line you must use to invoke it is a little different from other GATK tools (see usage below), and it does not accept any of the classic "CommandLineGATK" arguments.
java -cp GenomeAnalysisTK.jar org.broadinstitute.sting.tools.ListAnnotations
This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.
|--log_to_file||String||NA||Set the logging location|
|--logging_level||String||INFO||Set the minimum level of logging, i.e. setting INFO get's you INFO up to FATAL, setting ERROR gets you ERROR and FATAL level logging.|
|--help||Boolean||false||Generate this help message|
|--version||Boolean||false||Output version information|
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.
Generate this help message. this is used to indicate if they've asked for help
Set the logging location. where to send the output of our logger
Set the minimum level of logging, i.e. setting INFO get's you INFO up to FATAL, setting ERROR gets you ERROR and FATAL level logging.. the default log level
Output version information. This is used to indicate if they've asked for the version information
GATK version 2.8-1-g2a26ec9 built at 2013/12/06 16:54:02.