Package org.broadinstitute.hellbender.tools.walkers.vqsr

Class CNNVariantTrain

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.tools.walkers.vqsr.CNNVariantTrain

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@DocumentedFeature
@ExperimentalFeature
public class CNNVariantTrain
extends CommandLineProgram

Train a Convolutional Neural Network (CNN) for filtering variants. This tool expects requires training data generated by CNNVariantWriteTensors.

Inputs

• data-dir The training data created by CNNVariantWriteTensors.
• The --tensor-type argument determines what types of tensors the model will expect. Set it to "reference" for 1D tensors or "read_tensor" for 2D tensors.

Outputs

• output-dir The model weights file and semantic configuration json are saved here. This default to the current working directory.
• model-name The name for your model.

Usage example

Train a 1D CNN on Reference Tensors

 gatk CNNVariantTrain \
   -tensor-type reference \
   -input-tensor-dir my_tensor_folder \
   -model-name my_1d_model
 

Train a 2D CNN on Read Tensors

 gatk CNNVariantTrain \
   -input-tensor-dir my_tensor_folder \
   -tensor-type read-tensor \
   -model-name my_2d_model
 

Nested Class Summary

Nested classes/interfaces inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

CommandLineProgram.AutoCloseableNoCheckedExceptions

Field Summary

Fields inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

GATK_CONFIG_FILE, logger, NIO_MAX_REOPENS, NIO_PROJECT_FOR_REQUESTER_PAYS, QUIET, specialArgumentsCollection, tmpDir, useJdkDeflater, useJdkInflater, VERBOSITY

Constructor Summary

Constructors

Constructor	Description
CNNVariantTrain()

Method Summary

Modifier and Type	Method	Description
protected Object	doWork()	Do the work after command line has been parsed.
protected void	onStartup()	Perform initialization/setup after command-line argument parsing but before doWork() is invoked.

Methods inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getPluginDescriptors, getSupportInformation, getToolkitName, getToolkitShortName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, onShutdown, parseArgs, printLibraryVersions, printSettings, printStartupMessage, runTool, setDefaultHeaders, warnOnToolStatus

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

CNNVariantTrain

public CNNVariantTrain()

Method Details

onStartup

protected void onStartup()

Description copied from class: CommandLineProgram

Perform initialization/setup after command-line argument parsing but before doWork() is invoked. Default implementation does nothing. Subclasses can override to perform initialization.

Overrides:

onStartup in class CommandLineProgram

doWork

protected Object doWork()

Description copied from class: CommandLineProgram

Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.

Specified by:

doWork in class CommandLineProgram

Returns:

the return value or null is there is none.