Package org.broadinstitute.hellbender.tools.walkers.sv

Class CollectSVEvidence

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.GATKTool

org.broadinstitute.hellbender.engine.WalkerBase

org.broadinstitute.hellbender.engine.ReadWalker

org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@BetaFeature
@DocumentedFeature
public class CollectSVEvidence
extends ReadWalker

Creates discordant read pair, split read evidence, site depth, and read depth files for use in the GATK-SV pipeline. This tool emulates the functionality of the "svtk collect-pesr" used in v1 of the GATK-SV pipeline. The first output file, which should be named "*.pe.txt" or "*.pe.txt.gz" is a tab-delimited file containing information on discordant read pairs in the input cram, with the following columns:

• read contig
• read start
• read strand
• mate contig
• mate start
• mate strand
• sample name

Only one record is emitted for each discordant read pair, at the read in the pair with the "upstream" start position according to the sequence dictionary contig ordering and coordinate. The second output file, which should be named "*.sr.txt" or "*.sr.txt.gz" contains the locations of all split read clippings in the input bam or cram, with the following columns:

• contig
• clipping position
• direction: side of the read that was clipped (either "left" or "right")
• count: the number of reads clipped at this location in this direction
• sample name

The third output file, which should be named "*.sd.txt" or "*.sd.txt.gz" specifies site depth counts: For each locus specified in an input VCF as a simple, biallelic SNP, it gives a count, for each base call, of the number of reads that cover that locus. It has the following columns:

• contig
• position
• sampleName
• A observations
• C observations
• G observations
• T observations

The fourth output file, which should be named "*.rd.txt" or "*.rd.txt.gz" specifies read depths: For each interval specified by a 3-column, tab delimited input file, the number of reads that start in that interval are reported. It has the following columns:

• contig
• starting position
• ending position
• read count

Note: when only collecting RD evidence, users should consider providing the same interval list with -L as --depth-evidence-intervals in order to avoid processing unused reads outside the intervals. Each of these output files may also be written as a block-compressed interval file, rather than as a tab-delimited text file by specifying an output file name that ends with ".bci" rather than ".txt". These files are self-indexing, and contain complete header information including sample name(s) and a dictionary for the contigs.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static final class	CollectSVEvidence.BAFSiteIterator

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

CommandLineProgram.AutoCloseableNoCheckedExceptions

Field Summary

Fields

Modifier and Type	Field	Description
static final String	COMPRESSION_LEVEL_ARGUMENT_LONG_NAME
static final String	DEPTH_EVIDENCE_INTERVALS_INPUT_FILE_ARGUMENT_LONG_NAME
static final String	DEPTH_EVIDENCE_INTERVALS_INPUT_FILE_ARGUMENT_SHORT_NAME
static final String	DEPTH_EVIDENCE_OUTPUT_FILE_ARGUMENT_LONG_NAME
static final String	DEPTH_EVIDENCE_OUTPUT_FILE_ARGUMENT_SHORT_NAME
static final String	DEPTH_EVIDENCE_SUMMARY_FILE_ARGUMENT_LONG_NAME
static final String	DEPTH_EVIDENCE_SUMMARY_FILE_ARGUMENT_SHORT_NAME
GATKPath	depthEvidenceInputFilename
GATKPath	depthEvidenceOutputFilename
GATKPath	depthEvidenceSummaryFilename
static final String	MIN_DEPTH_EVIDENCE_MAPQ_ARGUMENT_NAME
static final String	MIN_SITE_DEPTH_BASEQ_ARGUMENT_NAME
static final String	MIN_SITE_DEPTH_MAPQ_ARGUMENT_NAME
int	minDepthEvidenceMapQ
int	minMapQ
int	minQ
static final String	PAIRED_END_FILE_ARGUMENT_LONG_NAME
static final String	PAIRED_END_FILE_ARGUMENT_SHORT_NAME
GATKPath	peFile
static final String	SAMPLE_NAME_ARGUMENT_LONG_NAME
static final String	SITE_DEPTH_INPUT_ARGUMENT_LONG_NAME
static final String	SITE_DEPTH_INPUT_ARGUMENT_SHORT_NAME
static final String	SITE_DEPTH_OUTPUT_ARGUMENT_LONG_NAME
static final String	SITE_DEPTH_OUTPUT_ARGUMENT_SHORT_NAME
GATKPath	siteDepthInputFilename
GATKPath	siteDepthOutputFilename
static final String	SPLIT_READ_FILE_ARGUMENT_LONG_NAME
static final String	SPLIT_READ_FILE_ARGUMENT_SHORT_NAME
GATKPath	srFile

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

FEATURE_CACHE_LOOKAHEAD

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

addOutputSAMProgramRecord, addOutputVCFCommandLine, cloudIndexPrefetchBuffer, cloudPrefetchBuffer, createOutputBamIndex, createOutputBamMD5, createOutputVariantIndex, createOutputVariantMD5, disableBamIndexCaching, features, 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	Description
CollectSVEvidence()

Method Summary

Modifier and Type	Method	Description
void	apply(GATKRead read, ReferenceContext referenceContext, FeatureContext featureContext)	Process an individual read (with optional contextual information).
void	closeTool()	This method is called by the GATK framework at the end of the GATKTool.doWork() template method.
void	countSplitRead(GATKRead read, PriorityQueue<org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence.SplitPos> splitCounts, FeatureSink<SplitReadEvidence> srWriter)	Adds split read information about the current read to the counts in splitCounts.
List<ReadFilter>	getDefaultReadFilters()	Returns the default list of CommandLineReadFilters that are used for this tool.
org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence.DiscordantRead	getReportableDiscordantReadPair(GATKRead read, Set<String> observedDiscordantNamesAtThisLocus, htsjdk.samtools.SAMSequenceDictionary samSequenceDictionary)
void	onTraversalStart()	Operations performed just prior to the start of traversal.
Object	onTraversalSuccess()	Operations performed immediately after a successful traversal (ie when no uncaught exceptions were thrown during the traversal).
boolean	requiresReads()	Does this tool require reads? Traversals types and/or tools that do should override to return true.

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

getProgressMeterRecordLabel, onShutdown, onStartup, resetReadsDataSource, traverse

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

directlyAccessEngineFeatureManager, directlyAccessEngineReadsDataSource, directlyAccessEngineReferenceDataSource

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

addFeatureInputsAfterInitialization, bamIndexCachingShouldBeEnabled, createSAMWriter, createVCFWriter, createVCFWriter, createVCFWriter, disableProgressMeter, doWork, getBestAvailableSequenceDictionary, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getGenomicsDBOptions, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolName, getTransformedReadStream, getTraversalIntervals, getUserSuppliedIntervals, hasFeatures, hasReads, hasReference, hasUserSuppliedIntervals, initializeProgressMeter, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeSamReaderFactory, makeVariantAnnotations, requiresFeatures, requiresIntervals, requiresReference, 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 Details

PAIRED_END_FILE_ARGUMENT_SHORT_NAME

public static final String PAIRED_END_FILE_ARGUMENT_SHORT_NAME

See Also:

• Constant Field Values

PAIRED_END_FILE_ARGUMENT_LONG_NAME

public static final String PAIRED_END_FILE_ARGUMENT_LONG_NAME

See Also:

• Constant Field Values

SPLIT_READ_FILE_ARGUMENT_SHORT_NAME

public static final String SPLIT_READ_FILE_ARGUMENT_SHORT_NAME

See Also:

• Constant Field Values

SPLIT_READ_FILE_ARGUMENT_LONG_NAME

public static final String SPLIT_READ_FILE_ARGUMENT_LONG_NAME

See Also:

• Constant Field Values

SITE_DEPTH_OUTPUT_ARGUMENT_SHORT_NAME

public static final String SITE_DEPTH_OUTPUT_ARGUMENT_SHORT_NAME

See Also:

• Constant Field Values

SITE_DEPTH_OUTPUT_ARGUMENT_LONG_NAME

public static final String SITE_DEPTH_OUTPUT_ARGUMENT_LONG_NAME

See Also:

• Constant Field Values

SITE_DEPTH_INPUT_ARGUMENT_SHORT_NAME

public static final String SITE_DEPTH_INPUT_ARGUMENT_SHORT_NAME

See Also:

• Constant Field Values

SITE_DEPTH_INPUT_ARGUMENT_LONG_NAME

public static final String SITE_DEPTH_INPUT_ARGUMENT_LONG_NAME

See Also:

• Constant Field Values

DEPTH_EVIDENCE_OUTPUT_FILE_ARGUMENT_SHORT_NAME

public static final String DEPTH_EVIDENCE_OUTPUT_FILE_ARGUMENT_SHORT_NAME

See Also:

• Constant Field Values

DEPTH_EVIDENCE_OUTPUT_FILE_ARGUMENT_LONG_NAME

public static final String DEPTH_EVIDENCE_OUTPUT_FILE_ARGUMENT_LONG_NAME

See Also:

• Constant Field Values

DEPTH_EVIDENCE_SUMMARY_FILE_ARGUMENT_SHORT_NAME

public static final String DEPTH_EVIDENCE_SUMMARY_FILE_ARGUMENT_SHORT_NAME

See Also:

• Constant Field Values

DEPTH_EVIDENCE_SUMMARY_FILE_ARGUMENT_LONG_NAME

public static final String DEPTH_EVIDENCE_SUMMARY_FILE_ARGUMENT_LONG_NAME

See Also:

• Constant Field Values

DEPTH_EVIDENCE_INTERVALS_INPUT_FILE_ARGUMENT_SHORT_NAME

public static final String DEPTH_EVIDENCE_INTERVALS_INPUT_FILE_ARGUMENT_SHORT_NAME

See Also:

• Constant Field Values

DEPTH_EVIDENCE_INTERVALS_INPUT_FILE_ARGUMENT_LONG_NAME

public static final String DEPTH_EVIDENCE_INTERVALS_INPUT_FILE_ARGUMENT_LONG_NAME

See Also:

• Constant Field Values

MIN_DEPTH_EVIDENCE_MAPQ_ARGUMENT_NAME

public static final String MIN_DEPTH_EVIDENCE_MAPQ_ARGUMENT_NAME

See Also:

• Constant Field Values

MIN_SITE_DEPTH_MAPQ_ARGUMENT_NAME

public static final String MIN_SITE_DEPTH_MAPQ_ARGUMENT_NAME

See Also:

• Constant Field Values

MIN_SITE_DEPTH_BASEQ_ARGUMENT_NAME

public static final String MIN_SITE_DEPTH_BASEQ_ARGUMENT_NAME

See Also:

• Constant Field Values

SAMPLE_NAME_ARGUMENT_LONG_NAME

public static final String SAMPLE_NAME_ARGUMENT_LONG_NAME

See Also:

• Constant Field Values

COMPRESSION_LEVEL_ARGUMENT_LONG_NAME

public static final String COMPRESSION_LEVEL_ARGUMENT_LONG_NAME

See Also:

• Constant Field Values

peFile

@Argument(shortName="PE",
          fullName="pe-file",
          doc="Output file for paired end evidence",
          optional=true)
public GATKPath peFile

srFile

@Argument(shortName="SR",
          fullName="sr-file",
          doc="Output file for split read evidence",
          optional=true)
public GATKPath srFile

siteDepthOutputFilename

@Argument(shortName="SD",
          fullName="sd-file",
          doc="Output file for site depth counts",
          optional=true)
public GATKPath siteDepthOutputFilename

siteDepthInputFilename

@Argument(shortName="F",
          fullName="site-depth-locs-vcf",
          doc="Input VCF of SNPs marking loci for site depth counts",
          optional=true)
public GATKPath siteDepthInputFilename

depthEvidenceOutputFilename

@Argument(shortName="RD",
          fullName="depth-evidence-file",
          doc="Output file for depth evidence",
          optional=true)
public GATKPath depthEvidenceOutputFilename

depthEvidenceSummaryFilename

@Argument(shortName="DS",
          fullName="depth-summary-file",
          doc="Output file for depth evidence summary statistics",
          optional=true)
public GATKPath depthEvidenceSummaryFilename

depthEvidenceInputFilename

@Argument(shortName="DI",
          fullName="depth-evidence-intervals",
          doc="Input feature file specifying intervals where depth evidence will be gathered",
          optional=true)
public GATKPath depthEvidenceInputFilename

minDepthEvidenceMapQ

@Argument(fullName="depth-evidence-min-mapq",
          doc="minimum mapping quality for read to be counted as depth evidence",
          optional=true)
public int minDepthEvidenceMapQ

minMapQ

@Argument(fullName="site-depth-min-mapq",
          doc="minimum mapping quality for read to be counted toward site depth",
          optional=true)
public int minMapQ

minQ

@Argument(fullName="site-depth-min-baseq",
          doc="minimum base call quality for SNP to be counted toward site depth",
          optional=true)
public int minQ

Constructor Details

CollectSVEvidence

public CollectSVEvidence()

Method Details

requiresReads

public boolean requiresReads()

Description copied from class: GATKTool

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

Overrides:

requiresReads in class ReadWalker

Returns:

true if this tool requires reads, 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

getDefaultReadFilters

public List<ReadFilter> getDefaultReadFilters()

Description copied from class: ReadWalker

Returns the default list of CommandLineReadFilters that are used for this tool. The filters returned by this method are subject to selective enabling/disabling by the user via the command line. The default implementation uses the WellformedReadFilter filter with all default options. Subclasses can override to provide alternative filters. Note: this method is called before command line parsing begins, and thus before a SAMFileHeader is available through {link #getHeaderForReads}.

Overrides:

getDefaultReadFilters in class ReadWalker

Returns:

List of individual filters to be applied for this tool.

apply

public void apply(GATKRead read,
 ReferenceContext referenceContext,
 FeatureContext featureContext)

Description copied from class: ReadWalker

Process an individual read (with optional contextual information). Must be implemented by tool authors. In general, tool authors should simply stream their output from apply(), and maintain as little internal state as possible. TODO: Determine whether and to what degree the GATK engine should provide a reduce operation TODO: to complement this operation. At a minimum, we should make apply() return a value to TODO: discourage statefulness in walkers, but how this value should be handled is TBD.

Specified by:

apply in class ReadWalker

Parameters:

read - current read

referenceContext - Reference bases spanning the current read. Will be an empty, but non-null, context object if there is no backing source of reference data (in which case all queries on it will return an empty array/iterator). Can request extra bases of context around the current read's interval by invoking ReferenceContext.setWindow(int, int) on this object before calling ReferenceContext.getBases()

featureContext - Features spanning the current read. Will be an empty, but non-null, context object if there is no backing source of Feature data (in which case all queries on it will return an empty List).

getReportableDiscordantReadPair

public org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence.DiscordantRead getReportableDiscordantReadPair(GATKRead read,
 Set<String> observedDiscordantNamesAtThisLocus,
 htsjdk.samtools.SAMSequenceDictionary samSequenceDictionary)

countSplitRead

public void countSplitRead(GATKRead read,
 PriorityQueue<org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence.SplitPos> splitCounts,
 FeatureSink<SplitReadEvidence> srWriter)

Adds split read information about the current read to the counts in splitCounts. Flushes split read counts to srWriter if necessary.

onTraversalSuccess

public 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

closeTool

public void closeTool()

Description copied from class: GATKTool

This method is called by the GATK framework at the end of the GATKTool.doWork() template method. It is called regardless of whether the GATKTool.traverse() has succeeded or not. It is called after the GATKTool.onTraversalSuccess() has completed (successfully or not) but before the GATKTool.doWork() method returns. In other words, on successful runs both GATKTool.onTraversalSuccess() and GATKTool.closeTool() will be called (in this order) while on failed runs (when GATKTool.traverse() causes an exception), only GATKTool.closeTool() will be called. The default implementation does nothing. Subclasses should override this method to close any resources that must be closed regardless of the success of traversal.

Overrides:

closeTool in class GATKTool