Class

dagr.tasks.gatk

Mutect2

Related Doc: package gatk

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class Mutect2 extends GatkTask with FixedResources

Task for running MuTect2 from the GATK 3.5+ distribution.

Linear Supertypes
GatkTask, Configuration, ConfigurationLike, FixedResources, ScheduleWithEmptyDefaultResources, JarTask, ProcessTask, UnitTask, Schedulable, LazyLogging, Task, Dependable, AnyRef, Any
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  2. By Inheritance
Inherited
  1. Mutect2
  2. GatkTask
  3. Configuration
  4. ConfigurationLike
  5. FixedResources
  6. ScheduleWithEmptyDefaultResources
  7. JarTask
  8. ProcessTask
  9. UnitTask
  10. Schedulable
  11. LazyLogging
  12. Task
  13. Dependable
  14. AnyRef
  15. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new Mutect2(tumorBam: PathToBam, normalBam: PathToBam, ref: PathToFasta, intervals: PathToIntervals, output: PathToVcf, maxAltAlleleInNormalFraction: Double = 0.03, maxAltAlleleInNormalCount: Int = 2, maxAltAlleleInNormalBqSum: Int = 20)

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Value Members

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

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    Definition Classes
    AnyRef → Any

  2. def !=>(other: Dependable): Unit

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    Definition Classes
    Task → Dependable

  3. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  4. def +(other: String): String

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    Implicit information
    This member is added by an implicit conversion from Mutect2 to any2stringadd[Mutect2] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

  5. def ->[B](y: B): (Mutect2, B)

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    Implicit information
    This member is added by an implicit conversion from Mutect2 to ArrowAssoc[Mutect2] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()

  6. def ::(other: Option[Dependable]): Dependable

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    Definition Classes
    Dependable

  7. def ::(other: Dependable): Dependable

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    Definition Classes
    Dependable

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

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    Definition Classes
    AnyRef → Any

  9. final def ==>(other: Option[Dependable]): Dependable

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    Definition Classes
    Dependable

  10. final def ==>(other: Dependable): Dependable

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    Definition Classes
    Dependable

  11. def addDependent(dependent: Dependable): Unit

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    Definition Classes
    Task → Dependable

  12. def addWalkerArgs(buffer: ListBuffer[Any]): Unit

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    Attributes
    protected
    Definition Classes
    Mutect2 → GatkTask

  13. def allTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  14. def applyResources(resources: ResourceSet): Unit

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    Definition Classes
    UnitTask → Schedulable

  15. def args: Seq[Any]

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    Definition Classes
    GatkTask → ProcessTask

  16. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  17. def asType[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  18. val bamCompression: Option[Int]

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    Definition Classes
    GatkTask

  19. def clone(): AnyRef

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

  20. def commandLineName(name: String): String

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    Definition Classes
    ConfigurationLike

  21. def config: Config

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    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike

  22. def configure[T](path: String, defaultValue: T)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

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    Definition Classes
    ConfigurationLike

  23. def configure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

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    Definition Classes
    ConfigurationLike

  24. def configureExecutable(path: String, executable: String): Path

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    Definition Classes
    ConfigurationLike

  25. def configureExecutableFromBinDirectory(binPath: String, executable: String, subDir: Option[Path]): Path

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    Definition Classes
    ConfigurationLike

  26. def ensuring(cond: (Mutect2) ⇒ Boolean, msg: ⇒ Any): Mutect2

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    Implicit information
    This member is added by an implicit conversion from Mutect2 to Ensuring[Mutect2] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  27. def ensuring(cond: (Mutect2) ⇒ Boolean): Mutect2

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    Implicit information
    This member is added by an implicit conversion from Mutect2 to Ensuring[Mutect2] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  28. def ensuring(cond: Boolean, msg: ⇒ Any): Mutect2

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    Implicit information
    This member is added by an implicit conversion from Mutect2 to Ensuring[Mutect2] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

  29. def ensuring(cond: Boolean): Mutect2

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    Implicit information
    This member is added by an implicit conversion from Mutect2 to Ensuring[Mutect2] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring

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

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    Definition Classes
    AnyRef

  31. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  32. def finalize(): Unit

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

  33. def formatted(fmtstr: String): String

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    Implicit information
    This member is added by an implicit conversion from Mutect2 to StringFormat[Mutect2] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()

  34. def gatkJar: Path

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    Can be overridden to use a specific GATK jar.

    Can be overridden to use a specific GATK jar.

    Attributes
    protected
    Definition Classes
    GatkTask

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

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    Definition Classes
    AnyRef → Any

  36. final def getTasks: Traversable[_ <: Mutect2.this.type]

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    Definition Classes
    UnitTask → Task

  37. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  38. def headTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  39. val intervals: Option[PathToIntervals]

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    Definition Classes
    GatkTask

  40. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  41. def jarArgs(jarPath: Path, jvmArgs: Traversable[String] = Nil, jvmProperties: Map[String, String] = Map.empty, jvmMemory: Memory, useAdvancedGcOptions: Boolean = true): List[String]

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    Attributes
    protected
    Definition Classes
    JarTask

  42. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  43. val maxAltAlleleInNormalBqSum: Int

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  44. val maxAltAlleleInNormalCount: Int

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  45. val maxAltAlleleInNormalFraction: Double

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  46. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  48. val normalBam: PathToBam

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  49. final def notify(): Unit

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    Definition Classes
    AnyRef

  50. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  51. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

  52. def optionallyConfigure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): Option[T]

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    Definition Classes
    ConfigurationLike

  53. val output: PathToVcf

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  54. def pickResources(availableResources: ResourceSet): Option[ResourceSet]

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    Definition Classes
    FixedResources → Schedulable

  55. var quoteIfNecessary: Boolean

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    Attributes
    protected
    Definition Classes
    ProcessTask

  56. val ref: PathToFasta

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    Definition Classes
    GatkTask

  57. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  58. def requires(cores: Double, memory: String): Mutect2.this.type

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    Definition Classes
    FixedResources

  59. def requires(cores: Cores, memory: Memory): Mutect2.this.type

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    Definition Classes
    FixedResources

  60. def requires(resources: ResourceSet): Mutect2.this.type

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    Definition Classes
    FixedResources

  61. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources

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

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    Definition Classes
    AnyRef

  63. def systemPath: Seq[Path]

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  64. def tailTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  65. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  66. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  67. def toString(): String

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    Definition Classes
    ProcessTask → AnyRef → Any

  68. val tumorBam: PathToBam

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  69. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  72. val walker: String

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    Definition Classes
    GatkTask

  73. def withName(name: String): Mutect2.this.type

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    Definition Classes
    Task

  74. def →[B](y: B): (Mutect2, B)

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    Implicit information
    This member is added by an implicit conversion from Mutect2 to ArrowAssoc[Mutect2] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from GatkTask

Inherited from Configuration

Inherited from ConfigurationLike

Inherited from FixedResources

Inherited from ScheduleWithEmptyDefaultResources

Inherited from JarTask

Inherited from ProcessTask

Inherited from UnitTask

Inherited from Schedulable

Inherited from LazyLogging

Inherited from Task

Inherited from Dependable

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion any2stringadd from Mutect2 to any2stringadd[Mutect2]

Inherited by implicit conversion StringFormat from Mutect2 to StringFormat[Mutect2]

Inherited by implicit conversion Ensuring from Mutect2 to Ensuring[Mutect2]

Inherited by implicit conversion ArrowAssoc from Mutect2 to ArrowAssoc[Mutect2]

Ungrouped