Package org.broadinstitute.hellbender.tools.sv

Class PrintSVEvidence

java.lang.Object
org.broadinstitute.hellbender.cmdline.CommandLineProgram
org.broadinstitute.hellbender.engine.GATKTool
org.broadinstitute.hellbender.engine.WalkerBase
org.broadinstitute.hellbender.engine.MultiFeatureWalker<SVFeature>
org.broadinstitute.hellbender.tools.sv.PrintSVEvidence
All Implemented Interfaces:
org.broadinstitute.barclay.argparser.CommandLinePluginProvider
@ExperimentalFeature public class PrintSVEvidence extends MultiFeatureWalker<SVFeature>

Merges locus-sorted files of evidence for structural variation into a single output file.

The tool can also subset the inputs to specified genomic intervals, or to a specified list of samples.

The evidence types and their files extensions are:

BafEvidence
The biallelic frequency of a SNP in some sample at some locus. File extensions are *.baf.txt, *.baf.txt.gz, or *.baf.bci.
DepthEvidence
The read counts of any number of samples on some interval. File extensions are *.rd.txt, *.rd.txt.gz, or *.rd.bci.
DiscordantPairEvidence
Evidence of a read pair that spans a genomic distance that's too large or too small. File extensions are *.pe.txt, *.pe.txt.gz, or *.pe.bci.
SiteDepth
The read counts of each base call for some sample at some locus. File extensions are *.sd.txt, *.sd.txt.gz, or *.sd.bci.
SplitReadEvidence
The number of chimeric reads in some sample at some locus. File extensions are *.sr.txt, *.sr.txt.gz, or *.sr.bci.

Inputs

  • One or more evidence files. These must be locus-sorted, and must all contain the same type of evidence.
    Or a file containing a list of evidence files, one per line.
  • Optional: A list of sample names to extract.

Output

  • An output file containing merged evidence from the inputs.

Usage example

     gatk SVCluster \
       -F file1.baf.txt.gz [-F file2.baf.txt.gz ...] \
       -O merged.baf.bci \
       --sample-names sample1 [--sample-names sample2 ...]

  • Field Details

  • Constructor Details

    • PrintSVEvidence

      public PrintSVEvidence()

  • Method Details

    • 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(SVFeature featureArg, Object header, ReadsContext readsContext, ReferenceContext referenceContext)
      Description copied from class: MultiFeatureWalker
      Process an individual feature. In general, subclasses should simply stream their output from apply(), and maintain as little internal state as possible.
      Specified by:
      apply in class MultiFeatureWalker<SVFeature>
      Parameters:
      featureArg - Current Feature being processed.
      header - Header object for the source from which the feature was drawn (may be null)
      readsContext - An object that allows querying for the reads the overlap the feature
      referenceContext - An object that allows querying for the reference sequence associated with the feature

    • 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