org.broadinstitute.hellbender.tools.walkers.contamination

Class GetPileupSummaries

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.GATKTool

org.broadinstitute.hellbender.engine.VariantWalkerBase

org.broadinstitute.hellbender.engine.MultiVariantWalker

org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@BetaFeature
 @DocumentedFeature
public class GetPileupSummaries
extends MultiVariantWalker

Summarizes counts of reads that support reference, alternate and other alleles for given sites. Results can be used with CalculateContamination.

The tool requires a common germline variant sites VCF, e.g. derived from the gnomAD resource, with population allele frequencies (AF) in the INFO field. This resource must contain only biallelic SNPs and can be an eight-column sites-only VCF. The tool ignores the filter status of the variant calls in this germline resource.

This tool is featured in the Somatic Short Mutation calling Best Practice Workflow. See Tutorial#11136 for a step-by-step description of the workflow and Article#11127 for an overview of what traditional somatic calling entails. For the latest pipeline scripts, see the Mutect2 WDL scripts directory. In particular, the mutect_resources.wdl script prepares a suitable resource from a larger dataset. An example excerpt is shown.

 #CHROM POS     ID      REF     ALT     QUAL    FILTER  INFO
 chr6   29942512        .       G       C       2974860 VQSRTrancheSNP99.80to99.90      AF=0.063
 chr6   29942517        .       C       A       2975860 VQSRTrancheSNP99.80to99.90      AF=0.062
 chr6   29942525        .       G       C       2975600 VQSRTrancheSNP99.60to99.80      AF=0.063
 chr6   29942547        rs114945359     G       C       15667700        PASS    AF=0.077
 

Usage examples

 gatk GetPileupSummaries \
   -I tumor.bam \
   -V common_biallelic.vcf.gz \
   -O pileups.table
 

 gatk GetPileupSummaries \
   -I normal.bam \
   -V common_biallelic.vcf.gz \
   -L chr1 \
   -O pileups.table
 

GetPileupSummaries tabulates results into six columns as shown below. The alt_count and allele_frequency correspond to the ALT allele in the germline resource.

 contig position        ref_count       alt_count       other_alt_count allele_frequency
 chr6   29942512        9       0       0       0.063
 chr6   29942517        13      1       0       0.062
 chr6   29942525        13      7       0       0.063
 chr6   29942547        36      0       0       0.077
 

Note the default maximum population AF (--maximum-population-allele-frequency or -max-af) is set to 0.2, which limits the sites the tool considers to those in the variants resource file that have AF of 0.2 or less. Likewise, the default minimum population AF (--minimum-population-allele-frequency or -min-af) is set to 0.01, which limits the sites the tool considers to those in the variants resource file that have AF of 0.01 or more.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	MAX_SITE_AF_LONG_NAME
static java.lang.String	MAX_SITE_AF_SHORT_NAME
static java.lang.String	MIN_MAPPING_QUALITY_LONG_NAME
static java.lang.String	MIN_MAPPING_QUALITY_SHORT_NAME
static java.lang.String	MIN_SITE_AF_LONG_NAME
static java.lang.String	MIN_SITE_AF_SHORT_NAME

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

drivingVariantFiles

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

FEATURE_CACHE_LOOKAHEAD

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

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

GATK_CONFIG_FILE, logger, NIO_MAX_REOPENS, QUIET, specialArgumentsCollection, TMP_DIR, useJdkDeflater, useJdkInflater, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
GetPileupSummaries()

Method Summary

Modifier and Type	Method and Description
void	apply(htsjdk.variant.variantcontext.VariantContext vc, ReadsContext readsContext, ReferenceContext referenceContext, FeatureContext featureContext) Process an individual variant.
java.util.List<ReadFilter>	getDefaultReadFilters() Returns the default list of ReadFilters that are used for this tool.
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	requiresReads() Does this tool require reads? 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.

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

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

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

getBestAvailableSequenceDictionary, getProgressMeterRecordLabel, makeVariantFilter, requiresFeatures, traverse

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

addFeatureInputsAfterInitialization, closeTool, createSAMWriter, createSAMWriter, createVCFWriter, doWork, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolkitShortName, getToolName, getTransformedReadStream, hasFeatures, hasIntervals, hasReads, hasReference, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeVariantAnnotations, requiresIntervals, useVariantAnnotations

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

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getSupportInformation, getToolkitName, 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

MAX_SITE_AF_LONG_NAME

public static final java.lang.String MAX_SITE_AF_LONG_NAME

See Also:

Constant Field Values

MIN_SITE_AF_LONG_NAME

public static final java.lang.String MIN_SITE_AF_LONG_NAME

See Also:

Constant Field Values

MAX_SITE_AF_SHORT_NAME

public static final java.lang.String MAX_SITE_AF_SHORT_NAME

See Also:

Constant Field Values

MIN_SITE_AF_SHORT_NAME

public static final java.lang.String MIN_SITE_AF_SHORT_NAME

See Also:

Constant Field Values

MIN_MAPPING_QUALITY_LONG_NAME

public static final java.lang.String MIN_MAPPING_QUALITY_LONG_NAME

See Also:

Constant Field Values

MIN_MAPPING_QUALITY_SHORT_NAME

public static final java.lang.String MIN_MAPPING_QUALITY_SHORT_NAME

See Also:

Constant Field Values

Constructor Detail

GetPileupSummaries

public GetPileupSummaries()

Method Detail

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 GATKTool

Returns:

true if this tool requires reads, otherwise false

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

getDefaultReadFilters

public java.util.List<ReadFilter> getDefaultReadFilters()

Description copied from class: GATKTool

Returns the default list of ReadFilters 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 returns an empty list. 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 GATKTool.getHeaderForReads(). The actual SAMFileHeader is propagated to the read filters by GATKTool.makeReadFilter() after the filters have been merged with command line arguments.

Overrides:

getDefaultReadFilters in class GATKTool

Returns:

List of individual filters to be applied for this tool.

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

apply

public void apply(htsjdk.variant.variantcontext.VariantContext vc,
                  ReadsContext readsContext,
                  ReferenceContext referenceContext,
                  FeatureContext featureContext)

Description copied from class: VariantWalkerBase

Process an individual variant. 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.

Specified by:

apply in class VariantWalkerBase

Parameters:

vc - 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)

referenceContext - 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()

featureContext - 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).

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