org.broadinstitute.hellbender.tools.walkers.varianteval

Class AlleleFrequencyQC

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.GATKTool

org.broadinstitute.hellbender.engine.WalkerBase

org.broadinstitute.hellbender.engine.VariantWalkerBase

org.broadinstitute.hellbender.engine.MultiVariantWalker

org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval

org.broadinstitute.hellbender.tools.walkers.varianteval.AlleleFrequencyQC

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

public class AlleleFrequencyQC
extends VariantEval

This tool uses VariantEval to bin variants in Thousand Genomes by allele frequency. For each bin, we compare the expected allele frequency from Thousand Genomes with the observed allele frequency in the input VCF. This was designed with arrays in mind, as a way to discover potential bugs in our pipeline. It uses the results from VariantEval to generate a simplified metric that returns a modified chi squared statistic (sum of the squared difference between the two allele frequencies in each bin, allowing a constant variance) as well as its associated p-value. The original VariantEval results can be returned by giving the debug variable a filename.

Field Summary

Fields

Modifier and Type	Field and Description
protected double	allowedVariance
protected java.io.File	debugFile
protected java.io.File	metricOutput
protected java.lang.String	sample
protected double	threshold

Fields inherited from class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval

AFScale, compsProvided, dbsnp, evals, goldStandard, intervalsFile, IS_SINGLETON_KEY, keepSitesWithAC0, KNOWN_NAMES, knownCNVsFile, LIST, MENDELIAN_VIOLATION_QUAL_THRESHOLD, mergeEvals, MIN_PHASE_QUALITY, MODULES_TO_USE, NO_STANDARD_MODULES, NO_STANDARD_STRATIFICATIONS, outFile, ploidy, SAMPLE_EXPRESSIONS, SELECT_EXPS, SELECT_NAMES, STRATIFICATIONS_TO_USE, useCompAFStratifier

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

multiVariantInputArgumentCollection

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

DEFAULT_DRIVING_VARIANTS_LOOKAHEAD_BASES, genomicsDBOptions

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 and Description
AlleleFrequencyQC()

Method Summary

Modifier and Type	Method and Description
void	onTraversalStart() Initialize the stratifications, evaluations, evaluation contexts, and reporting object
java.lang.Object	onTraversalSuccess() Operations performed immediately after a successful traversal (ie when no uncaught exceptions were thrown during the traversal).

Methods inherited from class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval

apply, createEvaluationContext, doApply, getAFScale, getAllFamilyName, getAllSampleName, getCompAFStratifier, getComps, getContigNames, getEvals, getEvaluationContexts, getFamilyNamesForEvaluation, getFamilyNamesForStratification, getJexlExpressions, getKnownCNVsFile, getKnowns, getLogger, getMendelianViolationQualThreshold, getMinPhaseQuality, getMultiVariantInputArgumentCollection, getNameForInput, getnProcessedLoci, getNumberOfSamplesForEvaluation, getPluginDescriptors, getSampleDB, getSampleNamesForEvaluation, getSampleNamesForStratification, getSamplePloidy, ignoreAC0Sites, initializeDrivingVariants, isSubsettingToSpecificSamples

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

getDrivingVariantsFeatureInputs, getHeaderForVariants, getSamplesForVariants, getSequenceDictionaryForDrivingVariants, getSpliteratorForDrivingVariants, onShutdown, onStartup, traverse

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

getBestAvailableSequenceDictionary, getDrivingVariantCacheLookAheadBases, getGenomicsDBOptions, getProgressMeterRecordLabel, getTransformedVariantStream, getTransformedVariantStream, makePostVariantFilterTransformer, makePreVariantFilterTransformer, makeVariantFilter, requiresFeatures

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

directlyAccessEngineFeatureManager, directlyAccessEngineReadsDataSource, directlyAccessEngineReferenceDataSource

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

addFeatureInputsAfterInitialization, closeTool, createSAMWriter, createSAMWriter, createVCFWriter, createVCFWriter, doWork, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolName, getTransformedReadStream, getTraversalIntervals, hasFeatures, hasReads, hasReference, hasUserSuppliedIntervals, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeVariantAnnotations, requiresIntervals, requiresReads, 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 Detail

threshold

@Argument(shortName="pvalue-threshold",
          doc="Threshold to cut off the pvalue.")
protected double threshold

allowedVariance

@Argument(shortName="allowed-variance",
          doc="Variance allowed in calculating the modified chi squared statistic.")
protected double allowedVariance

debugFile

@Argument(shortName="debug-file",
          doc="File to save the results from variant eval for debugging",
          optional=true)
protected java.io.File debugFile

metricOutput

protected java.io.File metricOutput

sample

protected java.lang.String sample

Constructor Detail

AlleleFrequencyQC

public AlleleFrequencyQC()

Method Detail

onTraversalStart

public void onTraversalStart()

Description copied from class: VariantEval

Initialize the stratifications, evaluations, evaluation contexts, and reporting object

Overrides:

onTraversalStart in class VariantEval

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 VariantEval

Returns:

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