org.hammerlab.guacamole.jointcaller.annotation

InsufficientNormal

case class InsufficientNormal(parameters: Parameters, referenceReads: Int, totalReads: Int) extends Annotation with Product with Serializable

Annotation and filter for insufficient normal evidence to make a somatic variant call.

There are many times when we have too little variant evidence in the normal to make a germline call but too much to comfortably make a somatic call. This filter removes such calls.

parameters
referenceReads

number of reads matching reference allele in pooled normal dna

totalReads

total number of reads in pooled normal dna

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Instance Constructors

  1. new InsufficientNormal(parameters: Parameters, referenceReads: Int, totalReads: Int)

    parameters
    referenceReads

    number of reads matching reference allele in pooled normal dna

    totalReads

    total number of reads in pooled normal dna

Value Members

  1. final def !=(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  2. final def !=(arg0: Any): Boolean

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  5. final def ==(arg0: Any): Boolean

    Definition Classes
    Any

  6. def addInfoToVCF(builder: VariantContextBuilder): Unit

    update VCF with annotation fields

    update VCF with annotation fields

    Definition Classes
    Annotation

  7. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  8. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  9. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  10. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  11. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any

  12. val isFiltered: Boolean

    is this annotation a failing filter?

    is this annotation a failing filter?

    Definition Classes
    InsufficientNormal → Annotation

  13. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  14. val name: String

    Definition Classes
    InsufficientNormal → Annotation

  15. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  16. final def notify(): Unit

    Definition Classes
    AnyRef

  17. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  18. val parameters: Parameters

  19. val referenceReads: Int

    number of reads matching reference allele in pooled normal dna

  20. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
    AnyRef

  21. val totalReads: Int

    total number of reads in pooled normal dna

  22. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  23. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  24. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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Inherited from AnyRef

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