Class/Object

dagr.tasks.vc

FilterFreeBayesCalls

Related Docs: object FilterFreeBayesCalls | package vc

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class FilterFreeBayesCalls extends Task with Configuration with FixedResources

Applies various filters and ensures proper VCF formatting for variants produced by FreeBayes.

This application of tools follows the procedure in bcbio's use of FreeBayes: https://github.com/chapmanb/bcbio-nextgen/blob/master/bcbio/variation/freebayes.py Briefly, does the following in order: - fix ambiguous (IUPAC) reference base calls - remove alternate alleles that are not called in any sample - split MNP variants into multiple records - updates AC and NS - sort records using a fixed length window - standardizes the representation of variants using parsimony and left-alignment relative to the reference genome* - remove both duplicate and reference alternate alleles

* See: http://genome.sph.umich.edu/wiki/Variant_Normalization

* Tool Requirements: - vcflib (https://github.com/vcflib/vcflib - vt (https://github.com/atks/vt) - bcftools (https://samtools.github.io/bcftools/) - bgzip (https://github.com/samtools/htslib)

You can set the path to the various scripts and executables within the configuration, or make sure they are on your PATH.

Linear Supertypes
FixedResources, ScheduleWithEmptyDefaultResources, Schedulable, Configuration, ConfigurationLike, LazyLogging, Task, Dependable, AnyRef, Any
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Inherited
  1. FilterFreeBayesCalls
  2. FixedResources
  3. ScheduleWithEmptyDefaultResources
  4. Schedulable
  5. Configuration
  6. ConfigurationLike
  7. LazyLogging
  8. Task
  9. Dependable
  10. AnyRef
  11. 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 FilterFreeBayesCalls(in: PathToVcf, out: PathToVcf, ref: PathToFasta, compress: Boolean = true, somatic: Boolean = false, minQual: Int = 5)

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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 FilterFreeBayesCalls to any2stringadd[FilterFreeBayesCalls] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

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

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    Implicit information
    This member is added by an implicit conversion from FilterFreeBayesCalls to ArrowAssoc[FilterFreeBayesCalls] 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 allTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  13. def applyResources(resources: ResourceSet): Unit

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    Definition Classes
    FilterFreeBayesCalls → Schedulable

  14. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

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

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  16. def clone(): AnyRef

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

  17. def commandLineName(name: String): String

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    Definition Classes
    ConfigurationLike

  18. val compress: Boolean

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  19. def config: Config

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    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

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

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    Definition Classes
    ConfigurationLike

  24. def ensuring(cond: (FilterFreeBayesCalls) ⇒ Boolean, msg: ⇒ Any): FilterFreeBayesCalls

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

  25. def ensuring(cond: (FilterFreeBayesCalls) ⇒ Boolean): FilterFreeBayesCalls

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

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

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

  27. def ensuring(cond: Boolean): FilterFreeBayesCalls

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

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

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    Definition Classes
    AnyRef

  29. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  30. def finalize(): Unit

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

  31. def formatted(fmtstr: String): String

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

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

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    Definition Classes
    AnyRef → Any

  33. def getTasks: Traversable[_ <: Task]

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    Definition Classes
    FilterFreeBayesCalls → Task

  34. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  35. def headTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  36. val in: PathToVcf

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  37. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  38. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging

  39. val minQual: Int

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  40. var name: String

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    Definition Classes
    Task

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

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    Definition Classes
    AnyRef

  42. final def notify(): Unit

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    Definition Classes
    AnyRef

  43. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  44. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task

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

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    Definition Classes
    ConfigurationLike

  46. val out: PathToVcf

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

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    Definition Classes
    FixedResources → Schedulable

  48. val ref: PathToFasta

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  49. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task

  50. def requires(cores: Double, memory: String): FilterFreeBayesCalls.this.type

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    Definition Classes
    FixedResources

  51. def requires(cores: Cores, memory: Memory): FilterFreeBayesCalls.this.type

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    Definition Classes
    FixedResources

  52. def requires(resources: ResourceSet): FilterFreeBayesCalls.this.type

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    Definition Classes
    FixedResources

  53. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources

  54. val somatic: Boolean

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

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    Definition Classes
    AnyRef

  56. def systemPath: Seq[Path]

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    Attributes
    protected
    Definition Classes
    ConfigurationLike

  57. def tailTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable

  58. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  59. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  60. def toString(): String

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    Definition Classes
    AnyRef → Any

  61. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  64. def withName(name: String): FilterFreeBayesCalls.this.type

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    Definition Classes
    Task

  65. def →[B](y: B): (FilterFreeBayesCalls, B)

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

Inherited from FixedResources

Inherited from ScheduleWithEmptyDefaultResources

Inherited from Schedulable

Inherited from Configuration

Inherited from ConfigurationLike

Inherited from LazyLogging

Inherited from Task

Inherited from Dependable

Inherited from AnyRef

Inherited from Any

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

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

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

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

Ungrouped