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ListAnnotations

Utility program to print a list of available annotations

Category Help Utilities


Overview

This is a very simple utility tool that retrieves available annotations for use with tools such as UnifiedGenotyper, HaplotypeCaller and VariantAnnotator.

Important note

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.

Usage

java -cp GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.ListAnnotations

Command-line Arguments

ListAnnotations 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 Outputs
--log_to_file
 -log
NA Set the logging location
Optional Parameters
--logging_level
 -l
INFO Set the minimum level of logging
Optional Flags
--help
 -h
false Generate the help message
--version
false Output version information

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.


--help / -h

Generate the help message
This will produce a help message in the terminal with general usage information, listing available arguments as well as tool-specific information if applicable.

Boolean  false


--log_to_file / -log

Set the logging location
File to save the logging output.

String


--logging_level / -l

Set the minimum level of logging
Setting INFO gets you INFO up to FATAL, setting ERROR gets you ERROR and FATAL level logging, and so on.

String  INFO


--version / -version

Output version information
Use this to check the version number of the GATK executable you are invoking. Note that the version number is always included in the output at the start of every run as well as any error message.

Boolean  false


See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA