org.broadinstitute.hellbender.tools.walkers.vqsr

Class GatherTranches

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.tools.walkers.vqsr.GatherTranches

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@BetaFeature
 @DocumentedFeature
public class GatherTranches
extends CommandLineProgram

Field Summary

Fields

Modifier and Type	Field and Description
java.util.List<java.io.File>	inputReports
org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorArgumentCollection.Mode	MODE Use either SNP for recalibrating only SNPs (emitting indels untouched in the output VCF) or INDEL for indels (emitting SNPs untouched in the output VCF).
java.io.File	outputReport

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 and Description
GatherTranches()

Method Summary

Modifier and Type	Method and Description
protected java.lang.Object	doWork() Do the work after command line has been parsed.

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, onStartup, 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

Field Detail

inputReports

@Argument(fullName="input",
          shortName="I",
          doc="List of scattered tranches files")
public final java.util.List<java.io.File> inputReports

MODE

@Argument(fullName="mode",
          shortName="mode",
          doc="Recalibration mode to employ")
public org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorArgumentCollection.Mode MODE

Use either SNP for recalibrating only SNPs (emitting indels untouched in the output VCF) or INDEL for indels (emitting SNPs untouched in the output VCF). There is also a BOTH option for recalibrating both SNPs and indels simultaneously, but this is meant for testing purposes only and should not be used in actual analyses.

outputReport

@Argument(fullName="output",
          shortName="O",
          doc="File to output the gathered tranches file to")
public java.io.File outputReport

Constructor Detail

GatherTranches

public GatherTranches()

Method Detail

doWork

protected java.lang.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.