org.broadinstitute.hellbender.tools.spark.sv.evidence

Class ExtractSVEvidenceSpark

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram

org.broadinstitute.hellbender.engine.spark.GATKSparkTool

org.broadinstitute.hellbender.tools.spark.sv.evidence.ExtractSVEvidenceSpark

All Implemented Interfaces:

java.io.Serializable, org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@DocumentedFeature
 @BetaFeature
public final class ExtractSVEvidenceSpark
extends GATKSparkTool

(Internal) Extracts evidence of structural variations from reads

This tool is used in development and should not be of interest to most researchers. It repackages the first two steps of the structural variation workflow as a separate tool for the convenience of developers.

This tool examines a SAM/BAM/CRAM for reads, or groups of reads, that demonstrate evidence of a structural variation in the vicinity. It records this evidence as a group of text files in a specified output directory on Spark's HDFS file system.

Inputs

• A file of paired-end, aligned and coordinate-sorted reads.

Output

• A directory of text files describing the evidence for structural variation discovered.

Usage example

   gatk ExtractSVEvidenceSpark \
     -I input_reads.bam \
     -O hdfs://my_cluster-m:8020/output_directory
     --aligner-index-image ignored --kmers-to-ignore ignored
 

This tool can be run without explicitly specifying Spark options. That is to say, the given example command without Spark options will run locally. See Tutorial#10060 for an example of how to set up and run a Spark tool on a cloud Spark cluster.

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.broadinstitute.hellbender.engine.spark.GATKSparkTool

GATKSparkTool.ReadInputMergingPolicy

Field Summary

Fields inherited from class org.broadinstitute.hellbender.engine.spark.GATKSparkTool

addOutputVCFCommandLine, BAM_PARTITION_SIZE_LONG_NAME, bamPartitionSplitSize, CREATE_OUTPUT_BAM_SPLITTING_INDEX_LONG_NAME, createOutputBamIndex, createOutputBamSplittingIndex, createOutputVariantIndex, features, intervalArgumentCollection, NUM_REDUCERS_LONG_NAME, numReducers, OUTPUT_SHARD_DIR_LONG_NAME, readArguments, referenceArguments, sequenceDictionaryValidationArguments, SHARDED_OUTPUT_LONG_NAME, shardedOutput, shardedPartsDir, SPLITTING_INDEX_GRANULARITY, splittingIndexGranularity, USE_NIO, useNio

Fields inherited from class org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram

programName, SPARK_PROGRAM_NAME_LONG_NAME, sparkArgs

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
ExtractSVEvidenceSpark()

Method Summary

Modifier and Type	Method and Description
boolean	requiresReads() Does this tool require reads? Tools that do should override to return true.
protected void	runTool(org.apache.spark.api.java.JavaSparkContext ctx) Runs the tool itself after initializing and validating inputs.

Methods inherited from class org.broadinstitute.hellbender.engine.spark.GATKSparkTool

addReferenceFilesForSpark, addVCFsForSpark, editIntervals, getBestAvailableSequenceDictionary, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getGatkReadJavaRDD, getHeaderForReads, getIntervals, getPluginDescriptors, getReadInputMergingPolicy, getReads, getReadSourceHeaderMap, getReadSourceName, getRecommendedNumReducers, getReference, getReferenceSequenceDictionary, getReferenceWindowFunction, getSequenceDictionaryValidationArgumentCollection, getTargetPartitionSize, getUnfilteredReads, hasReads, hasReference, hasUserSuppliedIntervals, makeReadFilter, makeReadFilter, makeVariantAnnotations, requiresIntervals, requiresReference, runPipeline, useVariantAnnotations, validateSequenceDictionaries, writeReads, writeReads

Methods inherited from class org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram

afterPipeline, doWork, getProgramName

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

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, 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

Constructor Detail

ExtractSVEvidenceSpark

public ExtractSVEvidenceSpark()

Method Detail

requiresReads

public boolean requiresReads()

Description copied from class: GATKSparkTool

Does this tool require reads? Tools that do should override to return true.

Overrides:

requiresReads in class GATKSparkTool

Returns:

true if this tool requires reads, otherwise false

runTool

protected void runTool(org.apache.spark.api.java.JavaSparkContext ctx)

Description copied from class: GATKSparkTool

Runs the tool itself after initializing and validating inputs. Must be implemented by subclasses.

Specified by:

runTool in class GATKSparkTool

Parameters:

ctx - our Spark context