@DocumentedFeature public class RemoveNearbyIndels extends VariantWalker
This is a preprocessing step for the CRSP sensitivity validation truth data. For any pair of indels that are within a minimum allowed distance (given by --min-indel-spacing), both indels are removed, regardless of any intervening non-indel variants.
gatk RemoveNearbyIndels \ -V input.vcf \ -O output.vcf \ --min-indel-spacing 20Created by David Benjamin on 1/30/17.
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
MIN_INDEL_SPACING_NAME |
drivingVariantFileDEFAULT_DRIVING_VARIANTS_LOOKAHEAD_BASES, genomicsDBOptionsaddOutputSAMProgramRecord, addOutputVCFCommandLine, cloudIndexPrefetchBuffer, cloudPrefetchBuffer, createOutputBamIndex, createOutputBamMD5, createOutputVariantIndex, createOutputVariantMD5, disableBamIndexCaching, features, intervalArgumentCollection, lenientVCFProcessing, outputSitesOnlyVCFs, progressMeter, readArguments, referenceArguments, SECONDS_BETWEEN_PROGRESS_UPDATES_NAME, seqValidationArgumentsGATK_CONFIG_FILE, logger, NIO_MAX_REOPENS, NIO_PROJECT_FOR_REQUESTER_PAYS, QUIET, specialArgumentsCollection, tmpDir, useJdkDeflater, useJdkInflater, VERBOSITY| Constructor and Description |
|---|
RemoveNearbyIndels() |
| Modifier and Type | Method and Description |
|---|---|
void |
apply(htsjdk.variant.variantcontext.VariantContext vc,
ReadsContext readsContext,
ReferenceContext refContext,
FeatureContext fc)
Process an individual variant.
|
void |
closeTool()
This method is called by the GATK framework at the end of the
GATKTool.doWork() template method. |
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).
|
getDrivingVariantsFeatureInput, getHeaderForVariants, getSequenceDictionaryForDrivingVariants, getSpliteratorForDrivingVariants, initializeDrivingVariants, onShutdown, onStartup, traversegetBestAvailableSequenceDictionary, getDrivingVariantCacheLookAheadBases, getGenomicsDBOptions, getProgressMeterRecordLabel, getTransformedVariantStream, getTransformedVariantStream, makePostVariantFilterTransformer, makePreVariantFilterTransformer, makeVariantFilter, requiresFeaturesdirectlyAccessEngineFeatureManager, directlyAccessEngineReadsDataSource, directlyAccessEngineReferenceDataSourceaddFeatureInputsAfterInitialization, createSAMWriter, createVCFWriter, createVCFWriter, createVCFWriter, doWork, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolName, getTransformedReadStream, getTraversalIntervals, hasFeatures, hasReads, hasReference, hasUserSuppliedIntervals, initializeProgressMeter, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeVariantAnnotations, requiresIntervals, requiresReads, requiresReference, transformTraversalIntervals, useVariantAnnotationscustomCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getSupportInformation, getToolkitName, getToolkitShortName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, parseArgs, printLibraryVersions, printSettings, printStartupMessage, runTool, setDefaultHeaders, warnOnToolStatuspublic static final java.lang.String MIN_INDEL_SPACING_NAME
public void onTraversalStart()
GATKToolonTraversalStart in class GATKToolpublic void apply(htsjdk.variant.variantcontext.VariantContext vc,
ReadsContext readsContext,
ReferenceContext refContext,
FeatureContext fc)
VariantWalkerapply in class VariantWalkervc - Current variant being processed.readsContext - Reads overlapping the current variant. Will be an empty, but non-null, context object
if there is no backing source of reads data (in which case all queries on it will return
an empty array/iterator)refContext - Reference bases spanning the current variant. 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 variant's interval
by invoking ReferenceContext.setWindow(int, int)
on this object before calling ReferenceContext.getBases()fc - Features spanning the current variant. 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).public java.lang.Object onTraversalSuccess()
GATKToolonTraversalSuccess in class GATKToolpublic void closeTool()
GATKToolGATKTool.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.