Package org.broadinstitute.hellbender.tools.walkers.mutect

Class GetNormalArtifactData

java.lang.Object
org.broadinstitute.hellbender.cmdline.CommandLineProgram
org.broadinstitute.hellbender.engine.GATKTool
org.broadinstitute.hellbender.engine.WalkerBase
org.broadinstitute.hellbender.engine.LocusWalker
org.broadinstitute.hellbender.tools.walkers.mutect.GetNormalArtifactData
All Implemented Interfaces:
org.broadinstitute.barclay.argparser.CommandLinePluginProvider
@DocumentedFeature public class GetNormalArtifactData extends LocusWalker

Usage example

 gatk GetNormalArtifactData \
   -I tumor.bam \
   -I normal.bam \
   -normal normal_sample \
   -L intervals.list \
   -O normal-artifact.table

  • Field Details

    • normalSamples

      @Argument(fullName="normal-sample", shortName="normal", doc="BAM sample name of normal. May be URL-encoded as output by GetSampleName with -encode argument.") protected List<String> normalSamples

    • ERROR_PROB_NAME

      public static final String ERROR_PROB_NAME
      See Also:

    • errorProb

      @Argument(fullName="error-prob", doc="Error probability for p-values", optional=true) protected double errorProb

  • Constructor Details

    • GetNormalArtifactData

      public GetNormalArtifactData()

  • Method Details

    • requiresReads

      public boolean requiresReads()
      Description copied from class: LocusWalker
      LocusWalkers requires read sources
      Overrides:
      requiresReads in class LocusWalker
      Returns:
      true if this tool requires reads, otherwise false

    • requiresReference

      public boolean requiresReference()
      Description copied from class: GATKTool
      Does this tool require reference data? Traversals types and/or tools that do should override to return true.
      Overrides:
      requiresReference in class GATKTool
      Returns:
      true if this tool requires a reference, otherwise false

    • requiresIntervals

      public boolean requiresIntervals()
      Description copied from class: GATKTool
      Does this tool require intervals? Traversals types and/or tools that do should override to return true.
      Overrides:
      requiresIntervals in class GATKTool
      Returns:
      true if this tool requires intervals, otherwise false

    • requiresFeatures

      public boolean requiresFeatures()
      Description copied from class: GATKTool
      Does this tool require features? Traversals types and/or tools that do should override to return true.
      Overrides:
      requiresFeatures in class GATKTool
      Returns:
      true if this tool requires reads, otherwise false

    • getDefaultReadFilters

      public List<ReadFilter> getDefaultReadFilters()
      Description copied from class: LocusWalker
      Returns the default list of CommandLineReadFilters that are used for this tool. The filters returned by this method are subject to selective enabling/disabling by the user via the command line. The default implementation uses the WellformedReadFilter and ReadFilterLibrary.MappedReadFilter filter with all default options. Subclasses can override to provide alternative filters. Note: this method is called before command line parsing begins, and thus before a SAMFileHeader is available through {link #getHeaderForReads}.
      Overrides:
      getDefaultReadFilters in class LocusWalker
      Returns:
      List of individual filters to be applied for this tool.

    • onTraversalStart

      public void onTraversalStart()
      Description copied from class: GATKTool
      Operations performed just prior to the start of traversal. Should be overridden by tool authors who need to process arguments local to their tool or perform other kinds of local initialization. Default implementation does nothing.
      Overrides:
      onTraversalStart in class GATKTool

    • apply

      public void apply(AlignmentContext alignmentContext, ReferenceContext referenceContext, FeatureContext featureContext)
      Description copied from class: LocusWalker
      Process an individual AlignmentContext (with optional contextual information). Must be implemented by tool authors. In general, tool authors should simply stream their output from apply(), and maintain as little internal state as possible.
      Specified by:
      apply in class LocusWalker
      Parameters:
      alignmentContext - current alignment context
      referenceContext - Reference bases spanning the current locus. Will be an empty, but non-null, context object if there is no backing source of reference data (in which case all queries on it will return an empty array/iterator). Can request extra bases of context around the current locus by invoking ReferenceContext.setWindow(int, int) on this object before calling ReferenceContext.getBases()
      featureContext - Features spanning the current locus. Will be an empty, but non-null, context object if there is no backing source of Feature data (in which case all queries on it will return an empty List).

    • onTraversalSuccess

      public Object onTraversalSuccess()
      Description copied from class: GATKTool
      Operations performed immediately after a successful traversal (ie when no uncaught exceptions were thrown during the traversal). Should be overridden by tool authors who need to close local resources, etc., after traversal. Also allows tools to return a value representing the traversal result, which is printed by the engine. Default implementation does nothing and returns null.
      Overrides:
      onTraversalSuccess in class GATKTool
      Returns:
      Object representing the traversal result, or null if a tool does not return a value