org.broadinstitute.hellbender.tools.walkers.contamination

Class ContaminationModel

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel

public class ContaminationModel
extends java.lang.Object

This is the probabilistic contamination model that we use to distinguish homs from hets The model is similar to that of ContEst, in that it assumes that each contaminant read is independently drawn from the population. However, it also accounts for allelic CNVs and doesn't just apply to hom alt sites. Because this model makes assumptions about the form of contamination and doesn't model CNVs precisely (although it is robust to them in that they don't lead to bad solutions), we don't actually use it for the final contamination estimate. Instead, we learn the model, then use it to predict which sites are hom alts. It's important to do this right because contamination makes hom alts look more like hets, and allelic CNVs make hets look more like hom alts, hence distinguishing correctly is not trivial.

Field Summary

Fields

Modifier and Type	Field and Description
static int	HOM_ALT
static int	HOM_REF
static double	INITIAL_MAF_THRESHOLD
static double	MAF_STEP_SIZE
static double	MAF_TO_SWITCH_TO_HOM_REF
static double	MAF_TO_SWITCH_TO_UNSCRUPULOUS_HOM_REF
static double	MINIMUM_UNSCRUPULOUS_HOM_REF_ALT_FRACTION_THRESHOLD
static double	UNSCRUPULOUS_HOM_REF_ALLELE_FRACTION
static double	UNSCRUPULOUS_HOM_REF_FRACTION_TO_REMOVE_FOR_POSSIBLE_LOH
static double	UNSCRUPULOUS_HOM_REF_PERCENTILE

Constructor Summary

Constructors

Constructor and Description
ContaminationModel(java.util.List<PileupSummary> sites)

Method Summary

Modifier and Type	Method and Description
org.apache.commons.lang3.tuple.Pair<java.lang.Double,java.lang.Double>	calculateContaminationFromHoms(java.util.List<PileupSummary> tumorSites) Calculate the contamination in a tumor sample using the hom alt and hom ref sites inferred from this model, which could be derived from the tumor itself or a matched normal.
java.util.List<MinorAlleleFractionRecord>	segmentationRecords()

Methods inherited from class java.lang.Object

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

Field Detail

INITIAL_MAF_THRESHOLD

public static final double INITIAL_MAF_THRESHOLD

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Constant Field Values

MAF_TO_SWITCH_TO_HOM_REF

public static final double MAF_TO_SWITCH_TO_HOM_REF

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Constant Field Values

MAF_TO_SWITCH_TO_UNSCRUPULOUS_HOM_REF

public static final double MAF_TO_SWITCH_TO_UNSCRUPULOUS_HOM_REF

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Constant Field Values

UNSCRUPULOUS_HOM_REF_ALLELE_FRACTION

public static final double UNSCRUPULOUS_HOM_REF_ALLELE_FRACTION

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Constant Field Values

UNSCRUPULOUS_HOM_REF_FRACTION_TO_REMOVE_FOR_POSSIBLE_LOH

public static final double UNSCRUPULOUS_HOM_REF_FRACTION_TO_REMOVE_FOR_POSSIBLE_LOH

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Constant Field Values

UNSCRUPULOUS_HOM_REF_PERCENTILE

public static final double UNSCRUPULOUS_HOM_REF_PERCENTILE

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Constant Field Values

MINIMUM_UNSCRUPULOUS_HOM_REF_ALT_FRACTION_THRESHOLD

public static final double MINIMUM_UNSCRUPULOUS_HOM_REF_ALT_FRACTION_THRESHOLD

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Constant Field Values

MAF_STEP_SIZE

public static final double MAF_STEP_SIZE

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Constant Field Values

HOM_REF

public static final int HOM_REF

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Constant Field Values

HOM_ALT

public static final int HOM_ALT

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Constant Field Values

Constructor Detail

ContaminationModel

public ContaminationModel(java.util.List<PileupSummary> sites)

Method Detail

calculateContaminationFromHoms

public org.apache.commons.lang3.tuple.Pair<java.lang.Double,java.lang.Double> calculateContaminationFromHoms(java.util.List<PileupSummary> tumorSites)

Calculate the contamination in a tumor sample using the hom alt and hom ref sites inferred from this model, which could be derived from the tumor itself or a matched normal.

Returns:

segmentationRecords

public java.util.List<MinorAlleleFractionRecord> segmentationRecords()