org.broadinstitute.hellbender.tools.walkers.mutect

Class Mutect2Engine

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine

All Implemented Interfaces:

AssemblyRegionEvaluator

public final class Mutect2Engine
extends java.lang.Object
implements AssemblyRegionEvaluator

Created by davidben on 9/15/16.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	CALLABLE_SITES_NAME
static int	HUGE_FRAGMENT_LENGTH
static int	INDEL_CONTINUATION_QUAL
static int	INDEL_START_QUAL
static double	MAX_ALT_FRACTION_IN_NORMAL
static int	MAX_NORMAL_QUAL_SUM
static int	MIN_PALINDROME_SIZE
static int	MINIMUM_BASE_QUALITY
static java.lang.String	NORMAL_SAMPLE_KEY_IN_VCF_HEADER
static java.lang.String	TUMOR_SAMPLE_KEY_IN_VCF_HEADER

Constructor Summary

Constructors

Constructor and Description
Mutect2Engine(M2ArgumentCollection MTAC, AssemblyRegionArgumentCollection assemblyRegionArgs, boolean createBamOutIndex, boolean createBamOutMD5, htsjdk.samtools.SAMFileHeader header, GATKPath referenceSpec, VariantAnnotatorEngine annotatorEngine) Create and initialize a new HaplotypeCallerEngine given a collection of HaplotypeCaller arguments, a reads header, and a reference file

Method Summary

Modifier and Type	Method and Description
java.util.List<htsjdk.variant.variantcontext.VariantContext>	callRegion(AssemblyRegion originalAssemblyRegion, ReferenceContext referenceContext, FeatureContext featureContext)
boolean	emitReferenceConfidence() Are we emitting a reference confidence in some form, or not?
static java.util.List<java.lang.Double>	getAttributeAsDoubleList(htsjdk.variant.variantcontext.VariantContext vc, java.lang.String key, double defaultValue)
static java.util.List<java.lang.Class<? extends Annotation>>	getStandardMutect2AnnotationGroups()
ActivityProfileState	isActive(AlignmentContext context, ReferenceContext ref, FeatureContext features) Given a pileup over a single locus, returns an ActivityProfileState containing the probability (0.0 to 1.0) that the locus is an "active" site.
static double	logLikelihoodRatio(int refCount, int altCount, double errorProbability)
static double	logLikelihoodRatio(int refCount, java.util.List<java.lang.Byte> altQuals)
static double	logLikelihoodRatio(int nRef, java.util.List<java.lang.Byte> altQuals, int repeatFactor)
static double	logLikelihoodRatio(int nRef, java.util.List<java.lang.Byte> altQuals, int repeatFactor, java.util.Optional<BetaDistributionShape> afPrior) this implements the isActive() algorithm described in docs/mutect/mutect.pdf the multiplicative factor is for the special case where we pass a singleton list of alt quals and want to duplicate that alt qual over multiple reads
static ReadTransformer	makeStandardMutect2PostFilterReadTransformer(java.nio.file.Path referencePath, boolean clipITRArtifacts)
static java.util.List<ReadFilter>	makeStandardMutect2ReadFilters()
void	shutdown()
protected java.util.Map<java.lang.String,java.util.List<GATKRead>>	splitReadsBySample(java.util.Collection<GATKRead> reads)
void	writeExtraOutputs(java.io.File statsTable)
void	writeHeader(htsjdk.variant.variantcontext.writer.VariantContextWriter vcfWriter, java.util.Set<htsjdk.variant.vcf.VCFHeaderLine> defaultToolHeaderLines)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

TUMOR_SAMPLE_KEY_IN_VCF_HEADER

public static final java.lang.String TUMOR_SAMPLE_KEY_IN_VCF_HEADER

See Also:

Constant Field Values

NORMAL_SAMPLE_KEY_IN_VCF_HEADER

public static final java.lang.String NORMAL_SAMPLE_KEY_IN_VCF_HEADER

See Also:

Constant Field Values

INDEL_START_QUAL

public static final int INDEL_START_QUAL

See Also:

Constant Field Values

INDEL_CONTINUATION_QUAL

public static final int INDEL_CONTINUATION_QUAL

See Also:

Constant Field Values

MAX_ALT_FRACTION_IN_NORMAL

public static final double MAX_ALT_FRACTION_IN_NORMAL

See Also:

Constant Field Values

MAX_NORMAL_QUAL_SUM

public static final int MAX_NORMAL_QUAL_SUM

See Also:

Constant Field Values

MIN_PALINDROME_SIZE

public static final int MIN_PALINDROME_SIZE

See Also:

Constant Field Values

HUGE_FRAGMENT_LENGTH

public static final int HUGE_FRAGMENT_LENGTH

See Also:

Constant Field Values

CALLABLE_SITES_NAME

public static final java.lang.String CALLABLE_SITES_NAME

See Also:

Constant Field Values

MINIMUM_BASE_QUALITY

public static final int MINIMUM_BASE_QUALITY

See Also:

Constant Field Values

Constructor Detail

Mutect2Engine

public Mutect2Engine(M2ArgumentCollection MTAC,
                     AssemblyRegionArgumentCollection assemblyRegionArgs,
                     boolean createBamOutIndex,
                     boolean createBamOutMD5,
                     htsjdk.samtools.SAMFileHeader header,
                     GATKPath referenceSpec,
                     VariantAnnotatorEngine annotatorEngine)

Create and initialize a new HaplotypeCallerEngine given a collection of HaplotypeCaller arguments, a reads header, and a reference file

Parameters:

MTAC - command-line arguments for the HaplotypeCaller

assemblyRegionArgs -

createBamOutIndex - true to create an index file for the bamout

createBamOutMD5 - true to create an md5 file for the bamout

header - header for the reads

referenceSpec - reference specifier for the reference

annotatorEngine - annotator engine built with desired annotations

Method Detail

makeStandardMutect2ReadFilters

public static java.util.List<ReadFilter> makeStandardMutect2ReadFilters()

makeStandardMutect2PostFilterReadTransformer

public static ReadTransformer makeStandardMutect2PostFilterReadTransformer(java.nio.file.Path referencePath,
                                                                           boolean clipITRArtifacts)

getStandardMutect2AnnotationGroups

public static java.util.List<java.lang.Class<? extends Annotation>> getStandardMutect2AnnotationGroups()

Returns:

the default set of variant annotations for Mutect2

writeHeader

public void writeHeader(htsjdk.variant.variantcontext.writer.VariantContextWriter vcfWriter,
                        java.util.Set<htsjdk.variant.vcf.VCFHeaderLine> defaultToolHeaderLines)

callRegion

public java.util.List<htsjdk.variant.variantcontext.VariantContext> callRegion(AssemblyRegion originalAssemblyRegion,
                                                                               ReferenceContext referenceContext,
                                                                               FeatureContext featureContext)

splitReadsBySample

protected java.util.Map<java.lang.String,java.util.List<GATKRead>> splitReadsBySample(java.util.Collection<GATKRead> reads)

writeExtraOutputs

public void writeExtraOutputs(java.io.File statsTable)

shutdown

public void shutdown()

isActive

public ActivityProfileState isActive(AlignmentContext context,
                                     ReferenceContext ref,
                                     FeatureContext features)

Description copied from interface: AssemblyRegionEvaluator

Given a pileup over a single locus, returns an ActivityProfileState containing the probability (0.0 to 1.0) that the locus is an "active" site.

Specified by:

isActive in interface AssemblyRegionEvaluator

Parameters:

context - reads pileup to examine

ref - reference base overlapping the pileup locus

features - features overlapping the pileup locus

Returns:

ActivityProfileState containing the probability between 0.0 and 1.0 that the site is active

getAttributeAsDoubleList

public static java.util.List<java.lang.Double> getAttributeAsDoubleList(htsjdk.variant.variantcontext.VariantContext vc,
                                                                        java.lang.String key,
                                                                        double defaultValue)

emitReferenceConfidence

public boolean emitReferenceConfidence()

Are we emitting a reference confidence in some form, or not?

Returns:

true if HC must emit reference confidence.

logLikelihoodRatio

public static double logLikelihoodRatio(int refCount,
                                        java.util.List<java.lang.Byte> altQuals)

logLikelihoodRatio

public static double logLikelihoodRatio(int nRef,
                                        java.util.List<java.lang.Byte> altQuals,
                                        int repeatFactor,
                                        java.util.Optional<BetaDistributionShape> afPrior)

this implements the isActive() algorithm described in docs/mutect/mutect.pdf the multiplicative factor is for the special case where we pass a singleton list of alt quals and want to duplicate that alt qual over multiple reads

Parameters:

nRef - ref read count

altQuals - Phred-scaled qualities of alt-supporting reads

repeatFactor - Number of times each alt qual is duplicated

afPrior - Beta prior on alt allele fraction

Returns:

logLikelihoodRatio

public static double logLikelihoodRatio(int nRef,
                                        java.util.List<java.lang.Byte> altQuals,
                                        int repeatFactor)

logLikelihoodRatio

public static double logLikelihoodRatio(int refCount,
                                        int altCount,
                                        double errorProbability)