org.broadinstitute.hellbender.tools.copynumber

Class AnnotateIntervals

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.GATKTool

org.broadinstitute.hellbender.tools.copynumber.AnnotateIntervals

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@DocumentedFeature
public final class AnnotateIntervals
extends GATKTool

Annotates intervals with GC content, and optionally, mappability and segmental-duplication content. The output may optionally be used as input to CreateReadCountPanelOfNormals, DenoiseReadCounts, and GermlineCNVCaller.

Inputs

• Reference FASTA file
• Intervals to be annotated. Supported formats are described in Article#1319. The argument interval-merging-rule must be set to IntervalMergingRule.OVERLAPPING_ONLY and all other common arguments for interval padding or merging must be set to their defaults.
• (Optional) Umap single-read mappability track. This is a BED file in .bed or .bed.gz format that identifies uniquely mappable regions of the genome. The track should correspond to the appropriate read length and overlapping intervals must be merged. See https://bismap.hoffmanlab.org/. If scores are provided, intervals will be annotated with the length-weighted average; note that NaN scores will be taken as unity. Otherwise, scores for covered and uncovered intervals will be taken as unity and zero, respectively.
• (Optional) Segmental-duplication track. This is a BED file in .bed or .bed.gz format that identifies segmental-duplication regions of the genome. Overlapping intervals must be merged. If scores are provided, intervals will be annotated with the length-weighted average; note that NaN scores will be taken as unity. Otherwise, scores for covered and uncovered intervals will be taken as unity and zero, respectively.

Output

• Annotated-intervals file. This is a tab-separated values (TSV) file with a SAM-style header containing a sequence dictionary, a row specifying the column headers for the contained annotations (see CopyNumberAnnotations for possible annotations), and the corresponding entry rows.

Usage examples

     gatk AnnotateIntervals \
          -R reference.fa \
          -L intervals.interval_list \
          --interval-merging-rule OVERLAPPING_ONLY \
          -O annotated_intervals.tsv
 

     gatk AnnotateIntervals \
          -R reference.fa \
          -L intervals.interval_list \
          --mappability-track mappability.bed.gz \
          --segmental-duplication-track segmental_duplication.bed.gz \
          --interval-merging-rule OVERLAPPING_ONLY \
          -O annotated_intervals.tsv
 

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	FEATURE_QUERY_LOOKAHEAD
static java.lang.String	MAPPABILITY_TRACK_PATH_LONG_NAME
static java.lang.String	SEGMENTAL_DUPLICATION_TRACK_PATH_LONG_NAME

Fields inherited from class org.broadinstitute.hellbender.engine.GATKTool

addOutputSAMProgramRecord, addOutputVCFCommandLine, cloudIndexPrefetchBuffer, cloudPrefetchBuffer, createOutputBamIndex, createOutputBamMD5, createOutputVariantIndex, createOutputVariantMD5, disableBamIndexCaching, intervalArgumentCollection, lenientVCFProcessing, outputSitesOnlyVCFs, progressMeter, readArguments, referenceArguments, SECONDS_BETWEEN_PROGRESS_UPDATES_NAME, seqValidationArguments

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
AnnotateIntervals()

Method Summary

Modifier and Type	Method and Description
void	onTraversalStart() Operations performed just prior to the start of traversal.
java.lang.Object	onTraversalSuccess() Operations performed immediately after a successful traversal (ie when no uncaught exceptions were thrown during the traversal).
boolean	requiresIntervals() Does this tool require intervals? Traversals types and/or tools that do should override to return true.
boolean	requiresReference() Does this tool require reference data? Traversals types and/or tools that do should override to return true.
void	traverse() A complete traversal from start to finish.

Methods inherited from class org.broadinstitute.hellbender.engine.GATKTool

addFeatureInputsAfterInitialization, closeTool, createSAMWriter, createSAMWriter, createVCFWriter, createVCFWriter, directlyAccessEngineFeatureManager, directlyAccessEngineReadsDataSource, directlyAccessEngineReferenceDataSource, doWork, getBestAvailableSequenceDictionary, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getGenomicsDBOptions, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getProgressMeterRecordLabel, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolName, getTransformedReadStream, getTraversalIntervals, hasFeatures, hasReads, hasReference, hasUserSuppliedIntervals, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeVariantAnnotations, onShutdown, onStartup, requiresFeatures, requiresReads, transformTraversalIntervals, useVariantAnnotations

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

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getSupportInformation, getToolkitName, getToolkitShortName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, 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

MAPPABILITY_TRACK_PATH_LONG_NAME

public static final java.lang.String MAPPABILITY_TRACK_PATH_LONG_NAME

See Also:

Constant Field Values

SEGMENTAL_DUPLICATION_TRACK_PATH_LONG_NAME

public static final java.lang.String SEGMENTAL_DUPLICATION_TRACK_PATH_LONG_NAME

See Also:

Constant Field Values

FEATURE_QUERY_LOOKAHEAD

public static final java.lang.String FEATURE_QUERY_LOOKAHEAD

See Also:

Constant Field Values

Constructor Detail

AnnotateIntervals

public AnnotateIntervals()

Method Detail

requiresReference

public boolean requiresReference()

Description copied from class: GATKTool

Does this tool require reference data? Traversals types and/or tools that do should override to return true.

Overrides:

requiresReference in class GATKTool

Returns:

true if this tool requires a reference, otherwise false

requiresIntervals

public boolean requiresIntervals()

Description copied from class: GATKTool

Does this tool require intervals? Traversals types and/or tools that do should override to return true.

Overrides:

requiresIntervals in class GATKTool

Returns:

true if this tool requires intervals, otherwise false

onTraversalStart

public void onTraversalStart()

Description copied from class: GATKTool

Operations performed just prior to the start of traversal. Should be overridden by tool authors who need to process arguments local to their tool or perform other kinds of local initialization. Default implementation does nothing.

Overrides:

onTraversalStart in class GATKTool

traverse

public void traverse()

Description copied from class: GATKTool

A complete traversal from start to finish. Tool authors who wish to "roll their own" traversal from scratch can extend this class directly and implement this method. Walker authors should instead extend a Walker class and implement the Walker-appropriate apply() method, since the Walker base classes implement the various kinds of traversals for you.

Specified by:

traverse in class GATKTool

onTraversalSuccess

public java.lang.Object onTraversalSuccess()

Description copied from class: GATKTool

Operations performed immediately after a successful traversal (ie when no uncaught exceptions were thrown during the traversal). Should be overridden by tool authors who need to close local resources, etc., after traversal. Also allows tools to return a value representing the traversal result, which is printed by the engine. Default implementation does nothing and returns null.

Overrides:

onTraversalSuccess in class GATKTool

Returns:

Object representing the traversal result, or null if a tool does not return a value