Package org.broadinstitute.hellbender.tools.copynumber

Class CallCopyRatioSegments

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.tools.copynumber.CallCopyRatioSegments

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@DocumentedFeature
public final class CallCopyRatioSegments
extends CommandLineProgram

Calls copy-ratio segments as amplified, deleted, or copy-number neutral.

This is a relatively naive caller that takes the modeled-segments output of ModelSegments and performs a simple statistical test on the segmented log2 copy ratios to call amplifications and deletions, given a specified range for determining copy-number neutral segments. This caller is based on the calling functionality of ReCapSeg.

If provided ModelSegments results that incorporate allele-fraction data, i.e. data with presumably improved segmentation, the statistical test performed by CallCopyRatioSegments ignores the modeled minor-allele fractions when making calls.

Input

• Copy-ratio-segments .cr.seg file from ModelSegments. This is a tab-separated values (TSV) file with a SAM-style header containing a read group sample name, a sequence dictionary, a row specifying the column headers contained in CopyRatioSegmentCollection.CopyRatioSegmentTableColumn, and the corresponding entry rows.

Outputs

• Called copy-ratio-segments file. This is a tab-separated values (TSV) file with a SAM-style header containing a read group sample name, a sequence dictionary, a row specifying the column headers contained in CalledCopyRatioSegmentCollection.CalledCopyRatioSegmentTableColumn, and the corresponding entry rows.
• CBS-formatted .igv.seg file (compatible with IGV). This is a tab-separated values (TSV) file with CBS-format column headers (see http://software.broadinstitute.org/cancer/software/genepattern/file-formats-guide#CBS) and the corresponding entry rows that can be plotted using IGV (see https://software.broadinstitute.org/software/igv/SEG). The mean log2 copy ratio is given in the SEGMENT_MEAN column.

Usage examples

     gatk CallCopyRatioSegments \
          -I tumor.cr.seg \
          -O tumor.called.seg
 

Nested Class Summary

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

CommandLineProgram.AutoCloseableNoCheckedExceptions

Field Summary

Fields

Modifier and Type	Field	Description
static final String	CALLING_COPY_RATIO_Z_SCORE_THRESHOLD_LONG_NAME
static final String	LEGACY_SEGMENTS_FILE_SUFFIX
static final String	NEUTRAL_SEGMENT_COPY_RATIO_LOWER_BOUND_LONG_NAME
static final String	NEUTRAL_SEGMENT_COPY_RATIO_UPPER_BOUND_LONG_NAME
static final String	OUTLIER_NEUTRAL_SEGMENT_COPY_RATIO_Z_SCORE_THRESHOLD_LONG_NAME

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
CallCopyRatioSegments()

Method Summary

Modifier and Type	Method	Description
protected 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 Details

NEUTRAL_SEGMENT_COPY_RATIO_LOWER_BOUND_LONG_NAME

public static final String NEUTRAL_SEGMENT_COPY_RATIO_LOWER_BOUND_LONG_NAME

See Also:

• Constant Field Values

NEUTRAL_SEGMENT_COPY_RATIO_UPPER_BOUND_LONG_NAME

public static final String NEUTRAL_SEGMENT_COPY_RATIO_UPPER_BOUND_LONG_NAME

See Also:

• Constant Field Values

OUTLIER_NEUTRAL_SEGMENT_COPY_RATIO_Z_SCORE_THRESHOLD_LONG_NAME

public static final String OUTLIER_NEUTRAL_SEGMENT_COPY_RATIO_Z_SCORE_THRESHOLD_LONG_NAME

See Also:

• Constant Field Values

CALLING_COPY_RATIO_Z_SCORE_THRESHOLD_LONG_NAME

public static final String CALLING_COPY_RATIO_Z_SCORE_THRESHOLD_LONG_NAME

See Also:

• Constant Field Values

LEGACY_SEGMENTS_FILE_SUFFIX

public static final String LEGACY_SEGMENTS_FILE_SUFFIX

See Also:

• Constant Field Values

Constructor Details

CallCopyRatioSegments

public CallCopyRatioSegments()

Method Details

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.