org.broadinstitute.hellbender.tools.walkers.annotator

Class PossibleDeNovo

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotation

org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation

org.broadinstitute.hellbender.tools.walkers.annotator.PedigreeAnnotation

org.broadinstitute.hellbender.tools.walkers.annotator.PossibleDeNovo

All Implemented Interfaces:

Annotation

@DocumentedFeature(groupName="Variant Annotations",
                   groupSummary="Available to HaplotypeCaller, Mutect2, VariantAnnotator and GenotypeGVCFs. See https://software.broadinstitute.org/gatk/documentation/article?id=10836",
                   summary="Existence of a de novo mutation in at least one of the given families (hiConfDeNovo, loConfDeNovo)")
public final class PossibleDeNovo
extends PedigreeAnnotation

Existence of a de novo mutation in at least one of the given families

This annotation uses the genotype information from individuals in family trios to identify possible de novo mutations and the sample(s) in which they occur. This works best if the genotypes have been processed according to the Genotype Refinement workflow.

Caveats

• The calculation assumes that the organism is diploid.
• This annotation requires a valid pedigree file.
• Only reports possible de novos for children whose genotypes have not been tagged as filtered (which is most appropriate if parent likelihoods have already been factored in using PhaseByTransmission).
• When multiple trios are present, the annotation is simply the maximum of the likelihood ratios, rather than the strict 1-Prod(1-p_i) calculation, as this can scale poorly for uncertain sites and many trios.
• This annotation can only be used from the Variant Annotator. If you attempt to use it from the UnifiedGenotyper, the run will fail with an error message to that effect. If you attempt to use it from the HaplotypeCaller, the run will complete successfully but the annotation will not be added to any variants.

Field Summary

Fields

Modifier and Type	Field and Description
static double	DEFAULT_MIN_GENOTYPE_QUALITY_P
protected org.apache.logging.log4j.Logger	warning

Fields inherited from class org.broadinstitute.hellbender.tools.walkers.annotator.PedigreeAnnotation

logger

Constructor Summary

Constructors

Constructor and Description
PossibleDeNovo()
PossibleDeNovo(GATKPath pedigreeFile)
PossibleDeNovo(java.util.Set<Trio> trios, double minGenotypeQualityP)

Method Summary

Modifier and Type	Method and Description
java.util.Map<java.lang.String,java.lang.Object>	annotate(ReferenceContext ref, htsjdk.variant.variantcontext.VariantContext vc, AlleleLikelihoods<GATKRead,htsjdk.variant.variantcontext.Allele> likelihoods) Computes the annotation for the given variant and the likelihoods per read.
java.util.List<java.lang.String>	getKeyNames() Return the keys

Methods inherited from class org.broadinstitute.hellbender.tools.walkers.annotator.PedigreeAnnotation

getFounderGenotypes, getTrios, setFounderIds, setPedigreeFile, validateArguments

Methods inherited from class org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation

getDescriptions

Methods inherited from class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotation

toString

Methods inherited from class java.lang.Object

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

Field Detail

warning

protected final org.apache.logging.log4j.Logger warning

DEFAULT_MIN_GENOTYPE_QUALITY_P

public static final double DEFAULT_MIN_GENOTYPE_QUALITY_P

See Also:

Constant Field Values

Constructor Detail

PossibleDeNovo

public PossibleDeNovo(java.util.Set<Trio> trios,
                      double minGenotypeQualityP)

PossibleDeNovo

public PossibleDeNovo(GATKPath pedigreeFile)

PossibleDeNovo

public PossibleDeNovo()

Method Detail

getKeyNames

public java.util.List<java.lang.String> getKeyNames()

Description copied from class: VariantAnnotation

Return the keys

Specified by:

getKeyNames in class VariantAnnotation

annotate

public java.util.Map<java.lang.String,java.lang.Object> annotate(ReferenceContext ref,
                                                                 htsjdk.variant.variantcontext.VariantContext vc,
                                                                 AlleleLikelihoods<GATKRead,htsjdk.variant.variantcontext.Allele> likelihoods)

Description copied from class: InfoFieldAnnotation

Computes the annotation for the given variant and the likelihoods per read. Returns a map from annotation keys to values (may be empty if no annotation is to be added).

Specified by:

annotate in class InfoFieldAnnotation

Parameters:

ref - Reference context, may be null

vc - Variant to be annotated. Not null.

likelihoods - likelihoods indexed by sample, allele, and read within sample