FreeBayes

Task for running FreeBayes, based on: https://github.com/chapmanb/bcbio-nextgen/blob/master/bcbio/variation/freebayes.py Does no pre-filtering for regions with high depth, but uses the --max-coverage option instead. Furthermore, no post-filtering of the calls are performed; see FilterFreeBayesCalls for applying post-calling filters.

regionSize will only be used if no interval list is given.

Tool Requirements: - freebayes (https://github.com/ekg/freebayes) - vcflib (https://github.com/vcflib/vcflib - bgzip (https://github.com/samtools/htslib) - parallel (http://www.gnu.org/software/parallel)

Other Requirements - reference FASTA must have an FAI

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

Please note that if the output VCF is a bgzip'ed VCF (vcf.gz) no index will be generated.

Linear Supertypes

VariableResources, ScheduleWithEmptyDefaultResources, Schedulable, Configuration, ConfigurationLike, LazyLogging, Task, Dependable, AnyRef, Any

Known Subclasses

FreeBayesGermline, FreeBayesSomatic

Instance Constructors

new FreeBayes(ref: PathToFasta, targetIntervals: Option[PathToIntervals], bam: List[PathToBam], vcf: PathToVcf, somatic: Boolean, compress: Boolean, memory: Memory, minThreads: Int, maxThreads: Int, regionSize: Long, useBestNAlleles: Option[Int], maxCoverage: Option[Int], minRepeatEntropy: Option[Int], minAlternateAlleleFraction: Option[Float] = None)

Value Members

final def !=(arg0: Any): Boolean

Definition Classes
AnyRef → Any
def !=>(other: MultiTask): other.type

Definition Classes
Task → Dependable
def !=>(other: Task): other.type

Definition Classes
Task → Dependable
final def ##(): Int

Definition Classes
AnyRef → Any
def +(other: String): String

Implicit information
This member is added by an implicit conversion from FreeBayes to any2stringadd[FreeBayes] performed by method any2stringadd in scala.Predef.
Definition Classes
any2stringadd
def ->[B](y: B): (FreeBayes, B)

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

Definition Classes
Task
final def ==(arg0: Any): Boolean

Definition Classes
AnyRef → Any
def ==>(other: MultiTask): other.type

Definition Classes
Task → Dependable
def ==>(other: Task): other.type

Definition Classes
Task → Dependable
def applyResources(resources: ResourceSet): Unit

Definition Classes
VariableResources → Schedulable
final def asInstanceOf[T0]: T0

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

Attributes
protected
Definition Classes
ConfigurationLike
val bam: List[PathToBam]
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
def commandLineName: String

Definition Classes
ConfigurationLike
val compress: Boolean
def config: Config

Attributes
protected
Definition Classes
Configuration → ConfigurationLike
def configure[T](path: String, defaultValue: T)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

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

Definition Classes
ConfigurationLike
def configureExecutable(path: String, executable: String): Path

Definition Classes
ConfigurationLike
def configureExecutableFromBinDirectory(binPath: String, executable: String): Path

Definition Classes
ConfigurationLike
def ensuring(cond: (FreeBayes) ⇒ Boolean, msg: ⇒ Any): FreeBayes

Implicit information
This member is added by an implicit conversion from FreeBayes to Ensuring[FreeBayes] performed by method Ensuring in scala.Predef.
Definition Classes
Ensuring
def ensuring(cond: (FreeBayes) ⇒ Boolean): FreeBayes

Implicit information
This member is added by an implicit conversion from FreeBayes to Ensuring[FreeBayes] performed by method Ensuring in scala.Predef.
Definition Classes
Ensuring
def ensuring(cond: Boolean, msg: ⇒ Any): FreeBayes

Implicit information
This member is added by an implicit conversion from FreeBayes to Ensuring[FreeBayes] performed by method Ensuring in scala.Predef.
Definition Classes
Ensuring
def ensuring(cond: Boolean): FreeBayes

Implicit information
This member is added by an implicit conversion from FreeBayes to Ensuring[FreeBayes] performed by method Ensuring in scala.Predef.
Definition Classes
Ensuring
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def equals(arg0: Any): Boolean

Definition Classes
AnyRef → Any
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
def formatted(fmtstr: String): String

Implicit information
This member is added by an implicit conversion from FreeBayes to StringFormat[FreeBayes] performed by method StringFormat in scala.Predef.
Definition Classes
StringFormat
Annotations
@inline()
final def getClass(): Class[_]

Definition Classes
AnyRef → Any
def getTasks: Traversable[_ <: Task]

Sets the arguments for FreeBayes.
Sets the arguments for FreeBayes. For somatic calling, there should be two bams, a tumor bam then normal bam.

Definition Classes
FreeBayes → Task
def hashCode(): Int

Definition Classes
AnyRef → Any
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
lazy val logger: Logger

Attributes
protected
Definition Classes
LazyLogging
val maxCoverage: Option[Int]
val maxThreads: Int
val memory: Memory
val minRepeatEntropy: Option[Int]
val minThreads: Int
var name: String

Definition Classes
Task
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
def numThreads: Int

Attributes
protected
def onComplete(exitCode: Int): Boolean

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

Definition Classes
ConfigurationLike
def pickResources(availableResources: ResourceSet): Option[ResourceSet]

Attempts to pick the resources required to run.
Attempts to pick the resources required to run. The required resources are: 1) Cores = the cores for freebayes plus one additional core to account for the other scripts 2) Memory = a fixed amount.

Definition Classes
FreeBayes → Schedulable
val ref: PathToFasta
val regionSize: Long
def removeDependency(task: Task): Boolean

Definition Classes
Task
def resources: ResourceSet

Definition Classes
ScheduleWithEmptyDefaultResources
def retry(taskInfo: TaskExecutionInfo, failedOnComplete: Boolean): Option[Task]

Definition Classes
Task
val somatic: Boolean
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def systemPath: Seq[Path]

Attributes
protected
Definition Classes
ConfigurationLike
val targetIntervals: Option[PathToIntervals]
def toString(): String

Definition Classes
AnyRef → Any
val useBestNAlleles: Option[Int]
val vcf: PathToVcf
final def wait(): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
final def wait(arg0: Long, arg1: Int): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
final def wait(arg0: Long): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
def withName(name: String): FreeBayes.this.type

Definition Classes
Task
def →[B](y: B): (FreeBayes, B)

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

Related Docs: object FreeBayes | package vc

abstract class FreeBayes extends Task with Configuration with VariableResources

Instance Constructors

Value Members

final def !=(arg0: Any): Boolean

def !=>(other: MultiTask): other.type

def !=>(other: Task): other.type

final def ##(): Int

def +(other: String): String

def ->[B](y: B): (FreeBayes, B)

def ::(other: Task): MultiTask

final def ==(arg0: Any): Boolean

def ==>(other: MultiTask): other.type

def ==>(other: Task): other.type

def applyResources(resources: ResourceSet): Unit

final def asInstanceOf[T0]: T0

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

val bam: List[PathToBam]

def clone(): AnyRef

def commandLineName: String

val compress: Boolean

def config: Config

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

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

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

def configureExecutableFromBinDirectory(binPath: String, executable: String): Path

def ensuring(cond: (FreeBayes) ⇒ Boolean, msg: ⇒ Any): FreeBayes

def ensuring(cond: (FreeBayes) ⇒ Boolean): FreeBayes

def ensuring(cond: Boolean, msg: ⇒ Any): FreeBayes

def ensuring(cond: Boolean): FreeBayes

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def finalize(): Unit

def formatted(fmtstr: String): String

final def getClass(): Class[_]

def getTasks: Traversable[_ <: Task]

def hashCode(): Int

final def isInstanceOf[T0]: Boolean

lazy val logger: Logger

val maxCoverage: Option[Int]

val maxThreads: Int

val memory: Memory

val minRepeatEntropy: Option[Int]

val minThreads: Int

var name: String

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

def numThreads: Int

def onComplete(exitCode: Int): Boolean

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

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

val ref: PathToFasta

val regionSize: Long

def removeDependency(task: Task): Boolean

def resources: ResourceSet

def retry(taskInfo: TaskExecutionInfo, failedOnComplete: Boolean): Option[Task]

val somatic: Boolean

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

def systemPath: Seq[Path]

val targetIntervals: Option[PathToIntervals]

def toString(): String

val useBestNAlleles: Option[Int]

val vcf: PathToVcf

final def wait(): Unit

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

final def wait(arg0: Long): Unit

def withName(name: String): FreeBayes.this.type

def →[B](y: B): (FreeBayes, B)

Inherited from VariableResources

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